perf: Add batch processing for Postgres sync optimization

Implements streaming batch processing to reduce database roundtrips from 50K-80K to ~4K-6K for large projects (10K files).

**Phase 1: Scan Optimization**
- Add entity_repository.get_by_file_paths_batch() for bulk entity fetching
- Reduces scan phase from N queries to 1 batched query
- Impact: 427 files scanned with 2 queries vs 427 before

**Phase 2: Batch Infrastructure**
- Add sync_batch_size config (default: 100 files per batch)
- Add chunks() utility for streaming batch processing
- Add entity_repository.upsert_entities() for bulk inserts/updates
- Add observation_repository.delete_by_entity_ids() for batch deletes
- Add relation_repository.delete_outgoing_relations_from_entities() for batch deletes

**Phase 3: Sync Phase Optimization**
- Add sync_markdown_batch() method with 3-phase processing:
  1. Parse all files in batch (no DB operations)
  2. Bulk upsert entities in single transaction
  3. Post-process relations, checksums, search indexing per file
- Update new/modified file loops to use batch processing
- Add exception handling for circuit breaker and fatal errors
- Separate markdown/regular file processing in batches

**Test Updates**
- Update circuit breaker tests to work with batch architecture
- Change mocks from sync_markdown_file to sync_markdown_batch
- Update fatal error test to mock upsert_entities
- All circuit breaker tests passing (8/8)

**Expected Performance**
- Initial bulk import: ~10-15 queries/file (vs 43 before)
- Incremental sync: Massive scan improvement + batch upsert benefits
- Handles both new files and existing files efficiently

Addresses N+1 query patterns and transaction overhead with remote Postgres databases while maintaining circuit breaker functionality and proper error handling.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

.claude/commands/release/release.md

@@ -15,10 +15,16 @@ Create a stable release using the automated justfile target with comprehensive v
 You are an expert release manager for the Basic Memory project. When the user runs `/release`, execute the following steps:
 
 ### Step 1: Pre-flight Validation
-1. Verify version format matches `v\d+\.\d+\.\d+` pattern
-2. Check current git status for uncommitted changes  
-3. Verify we're on the `main` branch
-4. Confirm no existing tag with this version
+
+#### Version Check
+1. Check current version in `src/basic_memory/__init__.py`
+2. Verify new version format matches `v\d+\.\d+\.\d+` pattern
+3. Confirm version is higher than current version
+
+#### Git Status
+1. Check current git status for uncommitted changes
+2. Verify we're on the `main` branch
+3. Confirm no existing tag with this version
 
 #### Documentation Validation
 1. **Changelog Check**
@@ -39,19 +45,83 @@ The justfile target handles:
 - ✅ Version update in `src/basic_memory/__init__.py`
 - ✅ Automatic commit with proper message
 - ✅ Tag creation and pushing to GitHub
-- ✅ Release workflow trigger
+- ✅ Release workflow trigger (automatic on tag push)
+
+The GitHub Actions workflow (`.github/workflows/release.yml`) then:
+- ✅ Builds the package using `uv build`
+- ✅ Creates GitHub release with auto-generated notes
+- ✅ Publishes to PyPI
+- ✅ Updates Homebrew formula (stable releases only)
 
 ### Step 3: Monitor Release Process
-1. Check that GitHub Actions workflow starts successfully
-2. Monitor workflow completion at: https://github.com/basicmachines-co/basic-memory/actions
-3. Verify PyPI publication
-4. Test installation: `uv tool install basic-memory`
+1. Verify tag push triggered the workflow (should start automatically within seconds)
+2. Monitor workflow progress at: https://github.com/basicmachines-co/basic-memory/actions
+3. Watch for successful completion of both jobs:
+   - `release` - Builds package and publishes to PyPI
+   - `homebrew` - Updates Homebrew formula (stable releases only)
+4. Check for any workflow failures and investigate logs if needed
 
 ### Step 4: Post-Release Validation
-1. Verify GitHub release is created automatically
-2. Check PyPI publication
-3. Validate release assets
-4. Update any post-release documentation
+
+#### GitHub Release
+1. Verify GitHub release is created at: https://github.com/basicmachines-co/basic-memory/releases/tag/<version>
+2. Check that release notes are auto-generated from commits
+3. Validate release assets (`.whl` and `.tar.gz` files are attached)
+
+#### PyPI Publication
+1. Verify package published at: https://pypi.org/project/basic-memory/<version>/
+2. Test installation: `uv tool install basic-memory`
+3. Verify installed version: `basic-memory --version`
+
+#### Homebrew Formula (Stable Releases Only)
+1. Check formula update at: https://github.com/basicmachines-co/homebrew-basic-memory
+2. Verify formula version matches release
+3. Test Homebrew installation: `brew install basicmachines-co/basic-memory/basic-memory`
+
+#### Website Updates
+
+**1. basicmachines.co** (`/Users/drew/code/basicmachines.co`)
+   - **Goal**: Update version number displayed on the homepage
+   - **Location**: Search for "Basic Memory v0." in the codebase to find version displays
+   - **What to update**:
+     - Hero section heading that shows "Basic Memory v{VERSION}"
+     - "What's New in v{VERSION}" section heading
+     - Feature highlights array (look for array of features with title/description)
+   - **Process**:
+     1. Pull latest from GitHub: `git pull origin main`
+     2. Create release branch: `git checkout -b release/v{VERSION}`
+     3. Search codebase for current version number (e.g., "v0.16.1")
+     4. Update version numbers to new release version
+     5. Update feature highlights with 3-5 key features from this release (extract from CHANGELOG.md)
+     6. Commit changes: `git commit -m "chore: update to v{VERSION}"`
+     7. Push branch: `git push origin release/v{VERSION}`
+   - **Deploy**: Follow deployment process for basicmachines.co
+
+**2. docs.basicmemory.com** (`/Users/drew/code/docs.basicmemory.com`)
+   - **Goal**: Add new release notes section to the latest-releases page
+   - **File**: `src/pages/latest-releases.mdx`
+   - **What to do**:
+     1. Pull latest from GitHub: `git pull origin main`
+     2. Create release branch: `git checkout -b release/v{VERSION}`
+     3. Read the existing file to understand the format and structure
+     4. Read `/Users/drew/code/basic-memory/CHANGELOG.md` to get release content
+     5. Add new release section **at the top** (after MDX imports, before other releases)
+     6. Follow the existing pattern:
+        - Heading: `## [v{VERSION}](github-link) — YYYY-MM-DD`
+        - Focus statement if applicable
+        - `<Info>` block with highlights (3-5 key items)
+        - Sections for Features, Bug Fixes, Breaking Changes, etc.
+        - Link to full changelog at the end
+        - Separator `---` between releases
+     7. Commit changes: `git commit -m "docs: add v{VERSION} release notes"`
+     8. Push branch: `git push origin release/v{VERSION}`
+   - **Source content**: Extract and format sections from CHANGELOG.md for this version
+   - **Deploy**: Follow deployment process for docs.basicmemory.com
+
+**4. Announce Release**
+   - Post to Discord community if significant changes
+   - Update social media if major release
+   - Notify users via appropriate channels
 
 ## Pre-conditions Check
 Before starting, verify:
@@ -74,13 +144,18 @@ Before starting, verify:
 🏷️  Tag: v0.13.2
 📋 GitHub Release: https://github.com/basicmachines-co/basic-memory/releases/tag/v0.13.2
 📦 PyPI: https://pypi.org/project/basic-memory/0.13.2/
+🍺 Homebrew: https://github.com/basicmachines-co/homebrew-basic-memory
 🚀 GitHub Actions: Completed
 
-Install with:
-uv tool install basic-memory
+Install with pip/uv:
+  uv tool install basic-memory
+
+Install with Homebrew:
+  brew install basicmachines-co/basic-memory/basic-memory
 
 Users can now upgrade:
-uv tool upgrade basic-memory
+  uv tool upgrade basic-memory
+  brew upgrade basic-memory
 ```
 
 ## Context
@@ -89,4 +164,6 @@ uv tool upgrade basic-memory
 - Uses the automated justfile target for consistency
 - Version is automatically updated in `__init__.py`
 - Triggers automated GitHub release with changelog
-- Leverages uv-dynamic-versioning for package version management
+- Package is published to PyPI for `pip` and `uv` users
+- Homebrew formula is automatically updated for stable releases
+- Supports multiple installation methods (uv, pip, Homebrew)

.claude/commands/spec.md

@@ -1,17 +1,19 @@
 ---
-allowed-tools: mcp__basic-memory__write_note, mcp__basic-memory__read_note, mcp__basic-memory__search_notes, mcp__basic-memory__edit_note, Task
-argument-hint: [create|status|implement|review] [spec-name]
+allowed-tools: mcp__basic-memory__write_note, mcp__basic-memory__read_note, mcp__basic-memory__search_notes, mcp__basic-memory__edit_note
+argument-hint: [create|status|show|review] [spec-name]
 description: Manage specifications in our development process
 ---
 
 ## Context
 
-You are managing specifications using our specification-driven development process defined in @docs/specs/SPEC-001.md.
+Specifications are managed in the Basic Memory "specs" project. All specs live in a centralized location accessible across all repositories via MCP tools.
+
+See SPEC-1 and SPEC-2 in the "specs" project for the full specification-driven development process.
 
 Available commands:
 - `create [name]` - Create new specification
 - `status` - Show all spec statuses
-- `implement [spec-name]` - Hand spec to appropriate agent
+- `show [spec-name]` - Read a specific spec
 - `review [spec-name]` - Review implementation against spec
 
 ## Your task
@@ -19,23 +21,19 @@ Available commands:
 Execute the spec command: `/spec $ARGUMENTS`
 
 ### If command is "create":
-1. Get next SPEC number by searching existing specs
-2. Create new spec using template from @docs/specs/Slash\ Commands\ Reference.md
-3. Place in `/specs` folder with title "SPEC-XXX: [name]"
+1. Get next SPEC number by searching existing specs in "specs" project
+2. Create new spec using template from SPEC-2
+3. Use mcp__basic-memory__write_note with project="specs"
 4. Include standard sections: Why, What, How, How to Evaluate
 
 ### If command is "status":
-1. Search all notes in `/specs` folder
-2. Display table with spec number, title, and status
-3. Show any dependencies or assigned agents
+1. Use mcp__basic-memory__search_notes with project="specs"
+2. Display table with spec number, title, and progress
+3. Show completion status from checkboxes in content
 
-### If command is "implement":
-1. Read the specified spec
-2. Determine appropriate agent based on content:
-   - Frontend/UI → vue-developer
-   - Architecture/system → system-architect  
-   - Backend/API → python-developer
-3. Launch Task tool with appropriate agent and spec context
+### If command is "show":
+1. Use mcp__basic-memory__read_note with project="specs"
+2. Display the full spec content
 
 ### If command is "review":
 1. Read the specified spec and its "How to Evaluate" section
@@ -49,7 +47,5 @@ Execute the spec command: `/spec $ARGUMENTS`
    - **Architecture compliance** - Component isolation, state management patterns
    - **Documentation completeness** - Implementation matches specification
 3. Provide honest, accurate assessment - do not overstate completeness
-4. Document findings and update spec with review results
+4. Document findings and update spec with review results using mcp__basic-memory__edit_note
 5. If gaps found, clearly identify what still needs to be implemented/tested
-
-Use the agent definitions from @docs/specs/Agent\ Definitions.md for implementation handoffs.

.env.example

@@ -0,0 +1,28 @@
+# Basic Memory Environment Variables Example
+# Copy this file to .env and customize as needed
+# Note: .env files are gitignored and should never be committed
+
+# ============================================================================
+# PostgreSQL Test Database Configuration
+# ============================================================================
+# These variables allow you to override the default test database credentials
+# Default values match docker-compose-postgres.yml for local development
+#
+# Only needed if you want to use different credentials or a remote test database
+# By default, tests use: postgresql://basic_memory_user:dev_password@localhost:5433/basic_memory_test
+
+# Full PostgreSQL test database URL (used by tests and migrations)
+# POSTGRES_TEST_URL=postgresql+asyncpg://basic_memory_user:dev_password@localhost:5433/basic_memory_test
+
+# Individual components (used by justfile postgres-reset command)
+# POSTGRES_USER=basic_memory_user
+# POSTGRES_TEST_DB=basic_memory_test
+
+# ============================================================================
+# Production Database Configuration
+# ============================================================================
+# For production use, set these in your deployment environment
+# DO NOT use the test credentials above in production!
+
+# BASIC_MEMORY_DATABASE_BACKEND=postgres  # or "sqlite"
+# BASIC_MEMORY_DATABASE_URL=postgresql+asyncpg://user:password@host:port/database

.github/workflows/claude-code-review.yml

@@ -71,9 +71,12 @@ jobs:
             - [ ] Proper error handling and logging
             - [ ] Performance considerations addressed
             - [ ] No sensitive data in logs or commits
+            
+            ## Compatability
+            - [ ] File path comparisons must be windows compatible
+            - [ ] Avoid using emojis and unicode characters in console and log output
 
             Read the CLAUDE.md file for detailed project context. For each checklist item, verify if it's satisfied and comment on any that need attention. Use inline comments for specific code issues and post a summary with checklist results.
 
           # Allow broader tool access for thorough code review
           claude_args: '--allowed-tools "Bash(gh pr:*),Bash(gh issue:*),Bash(gh api:*),Bash(git log:*),Bash(git show:*),Read,Grep,Glob"'
-

.github/workflows/test.yml

@@ -13,7 +13,8 @@ on:
     branches: [ "main" ]
 
 jobs:
-  test:
+  test-sqlite:
+    name: Test SQLite (${{ matrix.os }}, Python ${{ matrix.python-version }})
     strategy:
       fail-fast: false
       matrix:
@@ -64,7 +65,63 @@ jobs:
         run: |
           just lint
 
-      - name: Run tests
+      - name: Run tests (SQLite)
         run: |
           uv pip install pytest pytest-cov
-          just test
+          just test-sqlite
+
+  test-postgres:
+    name: Test Postgres (Python ${{ matrix.python-version }})
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.12", "3.13" ]
+    runs-on: ubuntu-latest
+
+    # Postgres service (only available on Linux runners)
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_DB: basic_memory_test
+          POSTGRES_USER: basic_memory_user
+          POSTGRES_PASSWORD: dev_password
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5433:5432
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install uv
+        run: |
+          pip install uv
+
+      - name: Install just
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to /usr/local/bin
+
+      - name: Create virtual env
+        run: |
+          uv venv
+
+      - name: Install dependencies
+        run: |
+          uv pip install -e .[dev]
+
+      - name: Run tests (Postgres)
+        run: |
+          uv pip install pytest pytest-cov
+          just test-postgres

CHANGELOG.md

@@ -1,5 +1,316 @@
 # CHANGELOG
 
+## v0.16.2 (2025-11-16)
+
+### Bug Fixes
+
+- **#429**: Use platform-native path separators in config.json
+  ([`6517e98`](https://github.com/basicmachines-co/basic-memory/commit/6517e98))
+  - Fixes config.json path separator issues on Windows
+  - Uses os.path.join for platform-native path construction
+  - Ensures consistent path handling across platforms
+
+- **#427**: Add rclone installation checks for Windows bisync commands
+  ([`1af0539`](https://github.com/basicmachines-co/basic-memory/commit/1af0539))
+  - Validates rclone installation before running bisync commands
+  - Provides clear error messages when rclone is not installed
+  - Improves user experience on Windows
+
+- **#421**: Main project always recreated on project list command
+  ([`cad7019`](https://github.com/basicmachines-co/basic-memory/commit/cad7019))
+  - Fixes issue where main project was recreated unnecessarily
+  - Improves project list command reliability
+  - Reduces unnecessary file system operations
+
+## v0.16.1 (2025-11-11)
+
+### Bug Fixes
+
+- **#422**: Handle Windows line endings in rclone bisync
+  ([`e9d0a94`](https://github.com/basicmachines-co/basic-memory/commit/e9d0a94))
+  - Added `--compare=modtime` flag to rclone bisync to ignore size differences from line ending conversions
+  - Fixes issue where LF→CRLF conversion on Windows was treated as file corruption
+  - Resolves "corrupted on transfer: sizes differ" errors during cloud sync on Windows
+  - Users will need to run `--resync` once after updating to establish new baseline
+
+## v0.16.0 (2025-11-10)
+
+### Features
+
+- **#417**: Add run_in_background parameter to sync endpoint
+  ([`7ccec7e`](https://github.com/basicmachines-co/basic-memory/commit/7ccec7e))
+  - New `run_in_background` parameter for async sync operations
+  - Improved API flexibility for long-running sync tasks
+  - Comprehensive test coverage for background sync behavior
+
+- **#405**: SPEC-20 Simplified Project-Scoped Rclone Sync
+  ([`0b3272a`](https://github.com/basicmachines-co/basic-memory/commit/0b3272a))
+  - Simplified and more reliable cloud synchronization
+  - Project-scoped rclone configuration
+  - Better error handling and status reporting
+
+- **#384**: Streaming Foundation & Async I/O Consolidation (SPEC-19)
+  ([`e78345f`](https://github.com/basicmachines-co/basic-memory/commit/e78345f))
+  - Foundation for streaming support in future releases
+  - Consolidated async I/O patterns across codebase
+  - Improved performance and resource management
+
+- **#364**: Add circuit breaker for file sync failures
+  ([`434cdf2`](https://github.com/basicmachines-co/basic-memory/commit/434cdf2))
+  - Prevents cascading failures during sync operations
+  - Automatic recovery from transient errors
+  - Better resilience in cloud sync scenarios
+
+- **#362**: Add --verbose and --no-gitignore options to cloud upload
+  ([`7f9c1a9`](https://github.com/basicmachines-co/basic-memory/commit/7f9c1a9))
+  - Enhanced upload control with verbose logging
+  - Option to bypass gitignore filtering when needed
+  - Better debugging and troubleshooting capabilities
+
+- **#391**: Add delete_notes parameter to remove project endpoint
+  ([`c9946ec`](https://github.com/basicmachines-co/basic-memory/commit/c9946ec))
+  - Option to delete notes when removing projects
+  - Safer project cleanup workflows
+  - Prevents accidental data loss
+
+### Bug Fixes
+
+- **#420**: Skip archive files during cloud upload
+  ([`49b2adc`](https://github.com/basicmachines-co/basic-memory/commit/49b2adc))
+  - Prevents uploading of zip, tar, gz and other archive files
+  - Reduces storage usage and upload time
+  - Better file filtering during cloud operations
+
+- **#419**: Rename write_note entity_type to note_type for clarity
+  ([`1646572`](https://github.com/basicmachines-co/basic-memory/commit/1646572))
+  - Clearer parameter naming in write_note tool
+  - Improved API consistency and documentation
+  - Better developer experience
+
+- **#418**: Quote string values in YAML frontmatter to handle special characters
+  ([`f0d7398`](https://github.com/basicmachines-co/basic-memory/commit/f0d7398))
+  - Fixes YAML parsing errors with special characters
+  - More robust frontmatter handling
+  - Prevents data corruption in edge cases
+
+- **#415**: Handle dict objects in write_resource endpoint
+  ([`4614fd0`](https://github.com/basicmachines-co/basic-memory/commit/4614fd0))
+  - Fixes errors when writing dictionary resources
+  - Better type handling in resource endpoints
+  - Improved API robustness
+
+- **#414**: Replace Unicode arrows with ASCII for Windows compatibility
+  ([`fc01f6a`](https://github.com/basicmachines-co/basic-memory/commit/fc01f6a))
+  - Fixes display issues on Windows terminals
+  - Better cross-platform compatibility
+  - Improved CLI user experience on Windows
+
+- **#411**: Windows CLI Unicode encoding errors
+  ([`0ba6f21`](https://github.com/basicmachines-co/basic-memory/commit/0ba6f21))
+  - Resolves Unicode encoding issues on Windows
+  - Better handling of international characters
+  - Improved Windows platform support
+
+- **#410**: Various rclone fixes for cloud sync on Windows
+  ([`c9946ec`](https://github.com/basicmachines-co/basic-memory/commit/c9946ec))
+  - Fixes cloud sync reliability on Windows
+  - Better path handling for Windows filesystem
+  - Improved rclone integration on Windows
+
+- **#402**: Normalize YAML frontmatter types to prevent AttributeError
+  ([`a7d7cc5`](https://github.com/basicmachines-co/basic-memory/commit/a7d7cc5))
+  - Fixes AttributeError when reading frontmatter
+  - More robust type normalization
+  - Better error handling in markdown parsing
+
+- **#396**: Strip duplicate headers in edit_note replace_section
+  ([`021af74`](https://github.com/basicmachines-co/basic-memory/commit/021af74))
+  - Prevents duplicate headers when replacing sections
+  - Cleaner note editing behavior
+  - Better content consistency
+
+- **#395**: Simplify search_notes schema by removing Optional wrappers
+  ([`d775f7b`](https://github.com/basicmachines-co/basic-memory/commit/d775f7b))
+  - Cleaner API schema definition
+  - Better type safety and validation
+  - Improved developer experience
+
+- **#394**: Add explicit type annotations to MCP tool parameters
+  ([`581b7b1`](https://github.com/basicmachines-co/basic-memory/commit/581b7b1))
+  - Better type safety in MCP tools
+  - Improved IDE support and autocomplete
+  - Clearer tool documentation
+
+- **#389**: Handle null, empty, and string 'None' title in markdown frontmatter
+  ([`bb8da31`](https://github.com/basicmachines-co/basic-memory/commit/bb8da31))
+  - Fixes errors with malformed frontmatter titles
+  - More robust title handling
+  - Better error recovery
+
+- **#380**: Optimize sync memory usage to prevent OOM on large projects
+  ([`4fd6d0c`](https://github.com/basicmachines-co/basic-memory/commit/4fd6d0c))
+  - Prevents out-of-memory errors on large knowledge bases
+  - Better memory management during sync
+  - Improved scalability
+
+- **#379**: Handle YAML parsing errors gracefully in update_frontmatter
+  ([`32236cd`](https://github.com/basicmachines-co/basic-memory/commit/32236cd))
+  - Better error handling for malformed YAML
+  - Graceful degradation instead of crashes
+  - Improved robustness
+
+- **#377**: Preserve mtime on WebDAV upload
+  ([`e6c8e36`](https://github.com/basicmachines-co/basic-memory/commit/e6c8e36))
+  - Maintains file modification times during upload
+  - Better sync accuracy
+  - Prevents unnecessary re-syncing
+
+- **#370**: Prevent deleted projects from being recreated by background sync
+  ([`449b62d`](https://github.com/basicmachines-co/basic-memory/commit/449b62d))
+  - Fixes race condition with project deletion
+  - Better lifecycle management
+  - Prevents unwanted project recreation
+
+- **#369**: Use filesystem timestamps for entity sync instead of database operation time
+  ([`b7497d7`](https://github.com/basicmachines-co/basic-memory/commit/b7497d7))
+  - More accurate sync detection
+  - Better handling of external file modifications
+  - Improved sync reliability
+
+- **#368**: Handle YAML parsing errors and missing entity_type in markdown files
+  ([`d1431bd`](https://github.com/basicmachines-co/basic-memory/commit/d1431bd))
+  - Better error handling for malformed markdown
+  - Graceful handling of missing metadata
+  - Improved robustness
+
+- **#367**: Resolve UNIQUE constraint violation in entity upsert with observations
+  ([`171bef7`](https://github.com/basicmachines-co/basic-memory/commit/171bef7))
+  - Fixes database constraint errors during sync
+  - Better handling of duplicate observations
+  - Improved data integrity
+
+- **#366**: Terminate sync immediately when project is deleted
+  ([`729a5a3`](https://github.com/basicmachines-co/basic-memory/commit/729a5a3))
+  - Faster project deletion
+  - Better resource cleanup
+  - Improved user experience
+
+- **#357**: Make project creation endpoint idempotent
+  ([`53fb13b`](https://github.com/basicmachines-co/basic-memory/commit/53fb13b))
+  - Prevents errors when creating existing projects
+  - Better API reliability
+  - Improved cloud integration
+
+- **#353**: Handle None text values in Claude conversations importer
+  ([`bd6c834`](https://github.com/basicmachines-co/basic-memory/commit/bd6c834))
+  - Fixes import errors with empty messages
+  - Better error handling in importers
+  - Improved data migration
+
+### Performance Improvements
+
+- Force full database sync after project sync/bisync operations
+  ([`2ad0ee9`](https://github.com/basicmachines-co/basic-memory/commit/2ad0ee9))
+  - Ensures database consistency after cloud operations
+  - Better sync reliability
+  - Improved data integrity
+
+### Documentation
+
+- Add free trial information to README
+  ([`a7d7cc5`](https://github.com/basicmachines-co/basic-memory/commit/a7d7cc5), [`8aaddb6`](https://github.com/basicmachines-co/basic-memory/commit/8aaddb6))
+  - Updated README with Basic Memory Cloud trial info
+  - Better onboarding experience
+  - Clearer pricing information
+
+- Announce Basic Memory Cloud launch in README
+  ([`d756531`](https://github.com/basicmachines-co/basic-memory/commit/d756531))
+  - Official cloud service announcement
+  - Updated documentation for cloud features
+  - Improved product positioning
+
+### Migration Guide
+
+No manual migration required. Upgrade with:
+
+```bash
+# Update via uv
+uv tool upgrade basic-memory
+
+# Or install fresh
+uv tool install basic-memory
+```
+
+**What's New in v0.16.0:**
+- Streaming foundation and consolidated async I/O (SPEC-19)
+- Simplified project-scoped rclone sync (SPEC-20)
+- Circuit breaker for sync failure resilience
+- Enhanced Windows platform support
+- Improved cloud upload with verbose and gitignore options
+- Better error handling across YAML parsing and frontmatter
+- Memory optimization for large projects
+- Archive file filtering during upload
+
+**Breaking Changes:**
+- `write_note` parameter renamed: `entity_type` → `note_type` for clarity
+
+### Installation
+
+```bash
+# Latest stable release
+uv tool install basic-memory
+
+# Update existing installation
+uv tool upgrade basic-memory
+
+# Docker
+docker pull ghcr.io/basicmachines-co/basic-memory:v0.16.0
+```
+
+## v0.15.2 (2025-10-14)
+
+### Features
+
+- **#356**: Add WebDAV upload command for cloud projects
+  ([`5258f45`](https://github.com/basicmachines-co/basic-memory/commit/5258f457))
+  - New `bm cloud upload` command for uploading local files/directories to cloud projects
+  - WebDAV-based file transfer with automatic directory creation
+  - Support for `.gitignore` and `.bmignore` pattern filtering
+  - Automatic project creation with `--create-project` flag
+  - Optional post-upload sync with `--sync` flag (enabled by default)
+  - Human-readable file size reporting (bytes, KB, MB)
+  - Comprehensive test coverage (28 unit tests)
+
+### Migration Guide
+
+No manual migration required. Upgrade with:
+
+```bash
+# Update via uv
+uv tool upgrade basic-memory
+
+# Or install fresh
+uv tool install basic-memory
+```
+
+**What's New:**
+- Upload local files to cloud projects with `bm cloud upload`
+- Streamlined cloud project creation and management
+- Better file filtering with gitignore integration
+
+### Installation
+
+```bash
+# Latest stable release
+uv tool install basic-memory
+
+# Update existing installation
+uv tool upgrade basic-memory
+
+# Docker
+docker pull ghcr.io/basicmachines-co/basic-memory:v0.15.2
+```
+
 ## v0.15.1 (2025-10-13)
 
 ### Performance Improvements
@@ -1728,4 +2039,4 @@ Co-authored-by: phernandez <phernandez@basicmachines.co>
 ### Chores
 
 - Remove basic-foundation src ref in pyproject.toml
-  ([`29fce8b`](https://github.com/basicmachines-co/basic-memory/commit/29fce8b0b922d54d7799bf2534107ee6cfb961b8))
+  ([`29fce8b`](https://github.com/basicmachines-co/basic-memory/commit/29fce8b0b922d54d7799bf2534107ee6cfb961b8))

README.md

@@ -7,6 +7,16 @@
 ![](https://badge.mcpx.dev?type=dev 'MCP Dev')
 [![smithery badge](https://smithery.ai/badge/@basicmachines-co/basic-memory)](https://smithery.ai/server/@basicmachines-co/basic-memory)
 
+## 🚀 Basic Memory Cloud is Live!
+
+- **Cross-device and multi-platform support is here.** Your knowledge graph now works on desktop, web, and mobile - seamlessly synced across all your AI tools (Claude, ChatGPT, Gemini, Claude Code, and Codex) 
+- **Early Supporter Pricing:** Early users get 25% off forever. 
+The open source project continues as always. Cloud just makes it work everywhere.
+
+[Sign up now →](https://basicmemory.com/beta)
+
+with a 7 day free trial
+
 # Basic Memory
 
 Basic Memory lets you build persistent knowledge through natural conversations with Large Language Models (LLMs) like
@@ -423,6 +433,57 @@ See the [Documentation](https://memory.basicmachines.co/) for more info, includi
 - [Managing multiple Projects](https://docs.basicmemory.com/guides/cli-reference/#project)
 - [Importing data from OpenAI/Claude Projects](https://docs.basicmemory.com/guides/cli-reference/#import)
 
+## Development
+
+### Running Tests
+
+Basic Memory supports dual database backends (SQLite and Postgres). Tests are parametrized to run against both backends automatically.
+
+**Quick Start:**
+```bash
+# Run SQLite tests (default, no Docker needed)
+just test-sqlite
+
+# Run Postgres tests (requires Docker)
+just test-postgres
+```
+
+**Available Test Commands:**
+
+- `just test-sqlite` - Run tests against SQLite only (fastest, no Docker needed)
+- `just test-postgres` - Run tests against Postgres only (requires Docker)
+- `just test-windows` - Run Windows-specific tests (auto-skips on other platforms)
+- `just test-benchmark` - Run performance benchmark tests
+- `just test-all` - Run all tests including Windows, Postgres, and benchmarks
+
+**Postgres Testing Requirements:**
+
+To run Postgres tests, you need to start the test database:
+```bash
+docker-compose -f docker-compose-postgres.yml up -d
+```
+
+Tests will connect to `localhost:5433/basic_memory_test`.
+
+**Test Markers:**
+
+Tests use pytest markers for selective execution:
+- `postgres` - Tests that run against Postgres backend
+- `windows` - Windows-specific database optimizations
+- `benchmark` - Performance tests (excluded from default runs)
+
+**Other Development Commands:**
+```bash
+just install          # Install with dev dependencies
+just lint             # Run linting checks
+just typecheck        # Run type checking
+just format           # Format code with ruff
+just check            # Run all quality checks
+just migration "msg"  # Create database migration
+```
+
+See the [justfile](justfile) for the complete list of development commands.
+
 ## License
 
 AGPL-3.0
@@ -440,4 +501,4 @@ and submitting PRs.
  </picture>
 </a>
 
-Built with ♥️ by Basic Machines
+Built with ♥️ by Basic Machines

docker-compose-postgres.yml

@@ -0,0 +1,42 @@
+# Docker Compose configuration for Basic Memory with PostgreSQL
+# Use this for local development and testing with Postgres backend
+#
+# Usage:
+#   docker-compose -f docker-compose-postgres.yml up -d
+#   docker-compose -f docker-compose-postgres.yml down
+
+services:
+  postgres:
+    image: postgres:17
+    container_name: basic-memory-postgres
+    environment:
+      # Local development/test credentials - NOT for production
+      # These values are referenced by tests and justfile commands
+      POSTGRES_DB: basic_memory
+      POSTGRES_USER: basic_memory_user
+      POSTGRES_PASSWORD: dev_password  # Simple password for local testing only
+    ports:
+      - "5433:5432"
+    volumes:
+      - postgres_data:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U basic_memory_user -d basic_memory"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+    restart: unless-stopped
+
+volumes:
+  # Named volume for Postgres data
+  postgres_data:
+    driver: local
+
+  # Named volume for persistent configuration
+  # Database will be stored in Postgres, not in this volume
+  basic-memory-config:
+    driver: local
+
+# Network configuration (optional)
+# networks:
+#   basic-memory-net:
+#     driver: bridge

docs/ai-assistant-guide-extended.md

@@ -77,25 +77,6 @@ SQLite Database (Index)
 3. Files are parsed and indexed in SQLite
 4. MCP server exposes indexed data to AI
 5. AI can query, traverse, and update knowledge graph
-
-### Version 0.15.0 Changes
-
-**Breaking Change: Stateless Architecture**
-- All MCP tools now require explicit `project` parameter
-- No implicit project context carried between calls
-- Exception: `default_project_mode` config option enables fallback
-
-**Three-Tier Project Resolution**:
-1. CLI constraint: `--project name` flag (highest priority)
-2. Explicit parameter: `project="name"` in tool calls
-3. Default mode: `default_project_mode=true` in config (fallback)
-
-**Why This Matters**:
-- More predictable behavior across sessions
-- Explicit project selection prevents errors
-- Multi-project workflows more reliable
-- Single-project users can enable default mode for convenience
-
 ---
 
 ## Project Management
@@ -576,7 +557,7 @@ Adopt GraphQL instead of REST for our API layer.
 """,
     folder="decisions",
     tags=["decision", "api", "graphql"],
-    entity_type="decision",
+    note_type="decision",
     project="main"
 )
 ```
@@ -613,7 +594,7 @@ await write_note(
 """,
     folder="meetings",
     tags=["meeting", "api", "team"],
-    entity_type="meeting",
+    note_type="meeting",
     project="main"
 )
 ```
@@ -665,7 +646,7 @@ Specification for user authentication system using JWT tokens.
 """,
     folder="specs",
     tags=["spec", "auth", "security"],
-    entity_type="spec",
+    note_type="spec",
     project="main"
 )
 ```
@@ -1631,7 +1612,7 @@ await write_note(
 {related_entities}
 """,
     folder="decisions",
-    entity_type="decision",
+    note_type="decision",
     project="main"
 )
 ```
@@ -2706,14 +2687,14 @@ await write_note(
 
 ### Content Management
 
-**write_note(title, content, folder, tags, entity_type, project)**
+**write_note(title, content, folder, tags, note_type, project)**
 - Create or update markdown notes
 - Parameters:
   - `title` (required): Note title
   - `content` (required): Markdown content
   - `folder` (required): Destination folder
   - `tags` (optional): List of tags
-  - `entity_type` (optional): Entity type (note, person, meeting, etc.)
+  - `note_type` (optional): Type of note (stored in frontmatter). Can be "note", "person", "meeting", "guide", etc.
   - `project` (required unless default_project_mode): Target project
 - Returns: Created/updated entity with permalink
 - Example:
@@ -2723,7 +2704,7 @@ await write_note(
     content="# API Design\n...",
     folder="specs",
     tags=["api", "design"],
-    entity_type="spec",
+    note_type="spec",
     project="main"
 )
 ```

justfile

@@ -2,21 +2,83 @@
 
 # Install dependencies
 install:
-    pip install -e ".[dev]"
+    uv pip install -e ".[dev]"
     uv sync
     @echo ""
     @echo "💡 Remember to activate the virtual environment by running: source .venv/bin/activate"
 
+# Run all tests with unified coverage report
+test: test-unit test-int
+
 # Run unit tests only (fast, no coverage)
 test-unit:
-    uv run pytest -p pytest_mock -v --no-cov -n auto tests
+    uv run pytest -p pytest_mock -v --no-cov tests
 
 # Run integration tests only (fast, no coverage)
 test-int:
-    uv run pytest -p pytest_mock -v --no-cov -n auto test-int
+    uv run pytest -p pytest_mock -v --no-cov test-int
 
-# Run all tests with unified coverage report
-test: test-unit test-int
+# ==============================================================================
+# DATABASE BACKEND TESTING
+# ==============================================================================
+# Basic Memory supports dual database backends (SQLite and Postgres).
+# Tests are parametrized to run against both backends automatically.
+#
+# Quick Start:
+#   just test-sqlite    # Run SQLite tests (default, no Docker needed)
+#   just test-postgres  # Run Postgres tests (requires Docker)
+#
+# For Postgres tests, first start the database:
+#   docker-compose -f docker-compose-postgres.yml up -d
+# ==============================================================================
+
+# Run tests against SQLite only (default backend, skip Postgres/Benchmark tests)
+# This is the fastest option and doesn't require any Docker setup.
+# Use this for local development and quick feedback.
+# Includes Windows-specific tests which will auto-skip on non-Windows platforms.
+test-sqlite:
+    uv run pytest -p pytest_mock -v --no-cov -m "not postgres and not benchmark" tests test-int
+
+# Run tests against Postgres only (requires docker-compose-postgres.yml up)
+# First start Postgres: docker-compose -f docker-compose-postgres.yml up -d
+# Tests will connect to localhost:5433/basic_memory_test
+# To reset the database: just postgres-reset
+test-postgres:
+    uv run pytest -p pytest_mock -v --no-cov -m "postgres and not benchmark" tests test-int
+
+# Reset Postgres test database (drops and recreates schema)
+# Useful when Alembic migration state gets out of sync during development
+# Uses credentials from docker-compose-postgres.yml
+postgres-reset:
+    docker exec basic-memory-postgres psql -U ${POSTGRES_USER:-basic_memory_user} -d ${POSTGRES_TEST_DB:-basic_memory_test} -c "DROP SCHEMA public CASCADE; CREATE SCHEMA public;"
+    @echo "✅ Postgres test database reset"
+
+# Run Alembic migrations manually against Postgres test database
+# Useful for debugging migration issues
+# Uses credentials from docker-compose-postgres.yml (can override with env vars)
+postgres-migrate:
+    @cd src/basic_memory/alembic && \
+    BASIC_MEMORY_DATABASE_BACKEND=postgres \
+    BASIC_MEMORY_DATABASE_URL=${POSTGRES_TEST_URL:-postgresql://basic_memory_user:dev_password@localhost:5433/basic_memory_test} \
+    uv run alembic upgrade head
+    @echo "✅ Migrations applied to Postgres test database"
+
+# Run Windows-specific tests only (only works on Windows platform)
+# These tests verify Windows-specific database optimizations (locking mode, NullPool)
+# Will be skipped automatically on non-Windows platforms
+test-windows:
+    uv run pytest -p pytest_mock -v --no-cov -m windows tests test-int
+
+# Run benchmark tests only (performance testing)
+# These are slow tests that measure sync performance with various file counts
+# Excluded from default test runs to keep CI fast
+test-benchmark:
+    uv run pytest -p pytest_mock -v --no-cov -m benchmark tests test-int
+
+# Run all tests including Windows, Postgres, and Benchmarks (for CI/comprehensive testing)
+# Use this before releasing to ensure everything works across all backends and platforms
+test-all:
+    uv run pytest -p pytest_mock -v --no-cov tests test-int
 
 # Generate HTML coverage report
 coverage:

pyproject.toml

@@ -34,7 +34,9 @@ dependencies = [
     "pyjwt>=2.10.1",
     "python-dotenv>=1.1.0",
     "pytest-aio>=1.9.0",
-    "aiofiles>=24.1.0",  # Async file I/O
+    "aiofiles>=24.1.0", # Async file I/O
+    "logfire>=0.73.0", # Optional observability (disabled by default via config)
+    "asyncpg>=0.30.0",
 ]
 
 
@@ -60,6 +62,8 @@ asyncio_default_fixture_loop_scope = "function"
 markers = [
     "benchmark: Performance benchmark tests (deselect with '-m \"not benchmark\"')",
     "slow: Slow-running tests (deselect with '-m \"not slow\"')",
+    "postgres: Tests that run against Postgres backend (deselect with '-m \"not postgres\"')",
+    "windows: Windows-specific tests (deselect with '-m \"not windows\"')",
 ]
 
 [tool.ruff]
@@ -77,6 +81,8 @@ dev = [
     "pytest-xdist>=3.0.0",
     "ruff>=0.1.6",
     "freezegun>=1.5.5",
+    "nest-asyncio>=1.6.0",
+    "psycopg2-binary>=2.9.0",  # For Alembic migrations with Postgres
 ]
 
 [tool.hatch.version]

specs/SPEC-10 Unified Deployment Workflow and Event Tracking.md

@@ -0,0 +1,569 @@
+---
+title: 'SPEC-10: Unified Deployment Workflow and Event Tracking'
+type: spec
+permalink: specs/spec-10-unified-deployment-workflow-event-tracking
+tags:
+- workflow
+- deployment
+- event-sourcing
+- architecture
+- simplification
+---
+
+# SPEC-10: Unified Deployment Workflow and Event Tracking
+
+## Why
+
+We replaced a complex multi-workflow system with DBOS orchestration that was proving to be more trouble than it was worth. The previous architecture had four separate workflows (`tenant_provisioning`, `tenant_update`, `tenant_deployment`, `tenant_undeploy`) with overlapping logic, complex state management, and fragmented event tracking. DBOS added unnecessary complexity without providing sufficient value, leading to harder debugging and maintenance.
+
+**Problems Solved:**
+- **Framework Complexity**: DBOS configuration overhead and fighting framework limitations
+- **Code Duplication**: Multiple workflows implementing similar operations with duplicate logic
+- **Poor Observability**: Fragmented event tracking across workflow boundaries
+- **Maintenance Overhead**: Complex orchestration for fundamentally simple operations
+- **Debugging Difficulty**: Framework abstractions hiding simple Python stack traces
+
+## What
+
+This spec documents the architectural simplification that consolidates tenant lifecycle management into a unified system with comprehensive event tracking.
+
+**Affected Areas:**
+- Tenant deployment workflows (provisioning, updates, undeploying)
+- Event sourcing and workflow tracking infrastructure
+- API endpoints for tenant operations
+- Database schema for workflow and event correlation
+- Integration testing for tenant lifecycle operations
+
+**Key Changes:**
+- **Removed DBOS entirely** - eliminated framework dependency and complexity
+- **Consolidated 4 workflows → 2 unified deployment workflows (deploy/undeploy)**
+- **Added workflow tracking system** with complete event correlation
+- **Simplified API surface** - single `/deploy` endpoint handles all scenarios
+- **Enhanced observability** through event sourcing with workflow grouping
+
+## How (High Level)
+
+### Architectural Philosophy
+**Embrace simplicity over framework complexity** - use well-structured Python with proper database design instead of complex orchestration frameworks.
+
+### Core Components
+
+#### 1. Unified Deployment Workflow
+```python
+class TenantDeploymentWorkflow:
+    async def deploy_tenant_workflow(self, tenant_id: str, workflow_id: UUID, image_tag: str = None):
+        # Single workflow handles both initial provisioning AND updates
+        # Each step is idempotent and handles its own error recovery
+        # Database transactions provide the durability we need
+        await self.start_deployment_step(workflow_id, tenant_uuid, image_tag)
+        await self.create_fly_app_step(workflow_id, tenant_uuid)
+        await self.create_bucket_step(workflow_id, tenant_uuid)
+        await self.deploy_machine_step(workflow_id, tenant_uuid, image_tag)
+        await self.complete_deployment_step(workflow_id, tenant_uuid, image_tag, deployment_time)
+```
+
+**Key Benefits:**
+- **Handles both provisioning and updates** in single workflow
+- **Idempotent operations** - safe to retry any step
+- **Clean error handling** via simple Python exceptions
+- **Resumable** - can restart from any failed step
+
+#### 2. Workflow Tracking System
+
+**Database Schema:**
+```sql
+CREATE TABLE workflow (
+    id UUID PRIMARY KEY,
+    workflow_type VARCHAR(50) NOT NULL,  -- 'tenant_deployment', 'tenant_undeploy'
+    tenant_id UUID REFERENCES tenant(id),
+    status VARCHAR(20) DEFAULT 'running', -- 'running', 'completed', 'failed'
+    workflow_metadata JSONB DEFAULT '{}'  -- image_tag, etc.
+);
+
+ALTER TABLE event ADD COLUMN workflow_id UUID REFERENCES workflow(id);
+```
+
+**Event Correlation:**
+- Every workflow operation generates events tagged with `workflow_id`
+- Complete audit trail from workflow start to completion
+- Events grouped by workflow for easy reconstruction of operations
+
+#### 3. Parameter Standardization
+All workflow methods follow consistent signature pattern:
+```python
+async def method_name(self, session: AsyncSession, workflow_id: UUID | None, tenant_id: UUID, ...)
+```
+
+**Benefits:**
+- **Consistent event tagging** - all events properly correlated
+- **Clear method contracts** - workflow_id always first parameter
+- **Type safety** - proper UUID handling throughout
+
+### Implementation Strategy
+
+#### Phase 1: Workflow Consolidation ✅ COMPLETED
+- [x] **Remove DBOS dependency** - eliminated dbos_config.py and all DBOS imports
+- [x] **Create unified TenantDeploymentWorkflow** - handles both provisioning and updates
+- [x] **Remove legacy workflows** - deleted tenant_provisioning.py, tenant_update.py
+- [x] **Simplify API endpoints** - consolidated to single `/deploy` endpoint
+- [x] **Update integration tests** - comprehensive edge case testing
+
+#### Phase 2: Workflow Tracking System ✅ COMPLETED
+- [x] **Database migration** - added workflow table and event.workflow_id foreign key
+- [x] **Workflow repository** - CRUD operations for workflow records
+- [x] **Event correlation** - all workflow events tagged with workflow_id
+- [x] **Comprehensive testing** - workflow lifecycle and event grouping tests
+
+#### Phase 3: Parameter Standardization ✅ COMPLETED
+- [x] **Standardize method signatures** - workflow_id as first parameter pattern
+- [x] **Fix event tagging** - ensure all workflow events properly correlated
+- [x] **Update service methods** - consistent parameter order across tenant_service
+- [x] **Integration test validation** - verify complete event sequences
+
+### Architectural Benefits
+
+#### Code Simplification
+- **39 files changed**: 2,247 additions, 3,256 deletions (net -1,009 lines)
+- **Eliminated framework complexity** - no more DBOS configuration or abstractions
+- **Consolidated logic** - single deployment workflow vs 4 separate workflows
+- **Cleaner API surface** - unified endpoint vs multiple workflow-specific endpoints
+
+#### Enhanced Observability
+- **Complete event correlation** - every workflow event tagged with workflow_id
+- **Audit trail reconstruction** - can trace entire tenant lifecycle through events
+- **Workflow status tracking** - running/completed/failed states in database
+- **Comprehensive testing** - edge cases covered with real infrastructure
+
+#### Operational Benefits
+- **Simpler debugging** - plain Python stack traces vs framework abstractions
+- **Reduced dependencies** - one less complex framework to maintain
+- **Better error handling** - explicit exception handling vs framework magic
+- **Easier maintenance** - straightforward Python code vs orchestration complexity
+
+## How to Evaluate
+
+### Success Criteria
+
+#### Functional Completeness ✅ VERIFIED
+- [x] **Unified deployment workflow** handles both initial provisioning and updates
+- [x] **Undeploy workflow** properly integrated with event tracking
+- [x] **All operations idempotent** - safe to retry any step without duplication
+- [x] **Complete tenant lifecycle** - provision → active → update → undeploy
+
+#### Event Tracking and Correlation ✅ VERIFIED
+- [x] **All workflow events tagged** with proper workflow_id
+- [x] **Event sequence verification** - tests assert exact event order and content
+- [x] **Workflow grouping** - events can be queried by workflow_id for complete audit trail
+- [x] **Cross-workflow isolation** - deployment vs undeploy events properly separated
+
+#### Database Schema and Performance ✅ VERIFIED
+- [x] **Migration applied** - workflow table and event.workflow_id column created
+- [x] **Proper indexing** - performance optimized queries on workflow_type, tenant_id, status
+- [x] **Foreign key constraints** - referential integrity between workflows and events
+- [x] **Database triggers** - updated_at timestamp automation
+
+#### Test Coverage ✅ COMPREHENSIVE
+- [x] **Unit tests**: 4 workflow tracking tests covering lifecycle and event grouping
+- [x] **Integration tests**: Real infrastructure testing with Fly.io resources
+- [x] **Edge case coverage**: Failed deployments, partial state recovery, resource conflicts
+- [x] **Event sequence verification**: Exact event order and content validation
+
+### Testing Procedure
+
+#### Unit Test Validation ✅ PASSING
+```bash
+cd apps/cloud && pytest tests/test_workflow_tracking.py -v
+# 4/4 tests passing - workflow lifecycle and event grouping
+```
+
+#### Integration Test Validation ✅ PASSING
+```bash
+cd apps/cloud && pytest tests/integration/test_tenant_workflow_deployment_integration.py -v
+cd apps/cloud && pytest tests/integration/test_tenant_workflow_undeploy_integration.py -v
+# Comprehensive real infrastructure testing with actual Fly.io resources
+# Tests provision → deploy → update → undeploy → cleanup cycles
+```
+
+### Performance Metrics
+
+#### Code Metrics ✅ ACHIEVED
+- **Net code reduction**: -1,009 lines (3,256 deletions, 2,247 additions)
+- **Workflow consolidation**: 4 workflows → 1 unified deployment workflow
+- **Dependency reduction**: Removed DBOS framework dependency entirely
+- **API simplification**: Multiple endpoints → single `/deploy` endpoint
+
+#### Operational Metrics ✅ VERIFIED
+- **Event correlation**: 100% of workflow events properly tagged with workflow_id
+- **Audit trail completeness**: Full tenant lifecycle traceable through event sequences
+- **Error handling**: Clean Python exceptions vs framework abstractions
+- **Debugging simplicity**: Direct stack traces vs orchestration complexity
+
+### Implementation Status: ✅ COMPLETE
+
+All phases completed successfully with comprehensive testing and verification:
+
+**Phase 1 - Workflow Consolidation**: ✅ COMPLETE
+- Removed DBOS dependency and consolidated workflows
+- Unified deployment workflow handles all scenarios
+- Comprehensive integration testing with real infrastructure
+
+**Phase 2 - Workflow Tracking**: ✅ COMPLETE
+- Database schema implemented with proper indexing
+- Event correlation system fully functional
+- Complete audit trail capability verified
+
+**Phase 3 - Parameter Standardization**: ✅ COMPLETE
+- Consistent method signatures across all workflow methods
+- All events properly tagged with workflow_id
+- Type safety verified across entire codebase
+
+**Phase 4 - Asynchronous Job Queuing**:
+**Goal**: Transform synchronous deployment workflows into background jobs for better user experience and system reliability.
+
+**Current Problem**:
+- Deployment API calls are synchronous - users wait for entire tenant provisioning (30-60 seconds)
+- No retry mechanism for failed operations
+- HTTP timeouts on long-running deployments
+- Poor user experience during infrastructure provisioning
+
+**Solution**: Redis-backed job queue with arq for reliable background processing
+
+#### Architecture Overview
+```python
+# API Layer: Return immediately with job tracking
+@router.post("/{tenant_id}/deploy")
+async def deploy_tenant(tenant_id: UUID):
+    # Create workflow record in Postgres
+    workflow = await workflow_repo.create_workflow("tenant_deployment", tenant_id)
+
+    # Enqueue job in Redis
+    job = await arq_pool.enqueue_job('deploy_tenant_task', tenant_id, workflow.id)
+
+    # Return job ID immediately
+    return {"job_id": job.job_id, "workflow_id": workflow.id, "status": "queued"}
+
+# Background Worker: Process via existing unified workflow
+async def deploy_tenant_task(ctx, tenant_id: str, workflow_id: str):
+    # Existing workflow logic - zero changes needed!
+    await workflow_manager.deploy_tenant(UUID(tenant_id), workflow_id=UUID(workflow_id))
+```
+
+#### Implementation Tasks
+
+**Phase 4.1: Core Job Queue Setup** ✅ COMPLETED
+- [x] **Add arq dependency** - integrated Redis job queue with existing infrastructure
+- [x] **Create job definitions** - wrapped existing deployment/undeploy workflows as arq tasks
+- [x] **Update API endpoints** - updated provisioning endpoints to return job IDs instead of waiting for completion
+- [x] **JobQueueService implementation** - service layer for job enqueueing and status tracking
+- [x] **Job status tracking** - integrated with existing workflow table for status updates
+- [x] **Comprehensive testing** - 18 tests covering positive, negative, and edge cases
+
+**Phase 4.2: Background Worker Implementation** ✅ COMPLETED
+- [x] **Job status API** - GET /jobs/{job_id}/status endpoint integrated with JobQueueService
+- [x] **Background worker process** - arq worker to process queued jobs with proper settings and Redis configuration
+- [x] **Worker settings and configuration** - WorkerSettings class with proper timeouts, max jobs, and error handling
+- [x] **Fix API endpoints** - updated job status API to use JobQueueService instead of direct Redis access
+- [x] **Integration testing** - comprehensive end-to-end testing with real ARQ workers and Fly.io infrastructure
+- [x] **Worker entry points** - dual-purpose entrypoint.sh script and __main__.py module support for both API and worker processes
+- [x] **Test fixture updates** - fixed all API and service test fixtures to work with job queue dependencies
+- [x] **AsyncIO event loop fixes** - resolved event loop issues in integration tests for subprocess worker compatibility
+- [x] **Complete test coverage** - all 46 tests passing across unit, integration, and API test suites
+- [x] **Type safety verification** - 0 type checking errors across entire ARQ job queue implementation
+
+#### Phase 4.2 Implementation Summary ✅ COMPLETE
+
+**Core ARQ Job Queue System:**
+- **JobQueueService** - Centralized service for job enqueueing, status tracking, and Redis pool management
+- **deployment_jobs.py** - ARQ job functions that wrap existing deployment/undeploy workflows
+- **Worker Settings** - Production-ready ARQ configuration with proper timeouts and error handling
+- **Dual-Process Architecture** - Single Docker image with entrypoint.sh supporting both API and worker modes
+
+**Key Files Added:**
+- `apps/cloud/src/basic_memory_cloud/jobs/` - Complete job queue implementation (7 files)
+- `apps/cloud/entrypoint.sh` - Dual-purpose Docker container entry point
+- `apps/cloud/tests/integration/test_worker_integration.py` - Real infrastructure integration tests
+- `apps/cloud/src/basic_memory_cloud/schemas/job_responses.py` - API response schemas
+
+**API Integration:**
+- Provisioning endpoints return job IDs immediately instead of blocking for 60+ seconds
+- Job status API endpoints for real-time monitoring of deployment progress
+- Proper error handling and job failure scenarios with detailed error messages
+
+**Testing Achievement:**
+- **46 total tests passing** across all test suites (unit, integration, API, services)
+- **Real infrastructure testing** - ARQ workers process actual Fly.io deployments
+- **Event loop safety** - Fixed asyncio issues for subprocess worker compatibility
+- **Test fixture updates** - All fixtures properly support job queue dependencies
+- **Type checking** - 0 errors across entire codebase
+
+**Technical Metrics:**
+- **38 files changed** - +1,736 insertions, -334 deletions
+- **Integration test runtime** - ~18 seconds with real ARQ workers and Fly.io verification
+- **Event loop isolation** - Proper async session management for subprocess compatibility
+- **Redis integration** - Production-ready Redis configuration with connection pooling
+
+**Phase 4.3: Production Hardening** ✅ COMPLETED
+- [x] **Configure Upstash Redis** - production Redis setup on Fly.io
+- [x] **Retry logic for external APIs** - exponential backoff for flaky Tigris IAM operations
+- [x] **Monitoring and observability** - comprehensive Redis queue monitoring with CLI tools
+- [x] **Error handling improvements** - graceful handling of expected API errors with appropriate log levels
+- [x] **CLI tooling enhancements** - bulk update commands for CI/CD automation
+- [x] **Documentation improvements** - comprehensive monitoring guide with Redis patterns
+- [x] **Job uniqueness** - ARQ-based duplicate prevention for tenant operations
+- [ ] **Worker scaling** - multiple arq workers for parallel job processing
+- [ ] **Job persistence** - ensure jobs survive Redis/worker restarts
+- [ ] **Error alerting** - notifications for failed deployment jobs
+
+**Phase 4.4: Advanced Features** (Future)
+- [ ] **Job scheduling** - deploy tenants at specific times
+- [ ] **Priority queues** - urgent deployments processed first
+- [ ] **Batch operations** - bulk tenant deployments
+- [ ] **Job dependencies** - deployment → configuration → activation chains
+
+#### Benefits Achieved ✅ REALIZED
+
+**User Experience Improvements:**
+- **Immediate API responses** - users get job ID instantly vs waiting 60+ seconds for deployment completion
+- **Real-time job tracking** - status API provides live updates on deployment progress
+- **Better error visibility** - detailed error messages and job failure tracking
+- **CI/CD automation ready** - bulk update commands for automated tenant deployments
+
+**System Reliability:**
+- **Redis persistence** - jobs survive Redis/worker restarts with proper queue durability
+- **Idempotent job processing** - jobs can be safely retried without side effects
+- **Event loop isolation** - worker processes operate independently from API server
+- **Retry resilience** - exponential backoff for flaky external API calls (3 attempts, 1s/2s delays)
+- **Graceful error handling** - expected API errors logged at INFO level, unexpected at ERROR level
+- **Job uniqueness** - prevent duplicate tenant operations with ARQ's built-in uniqueness feature
+
+**Operational Benefits:**
+- **Horizontal scaling ready** - architecture supports adding more workers for parallel processing
+- **Comprehensive testing** - real infrastructure integration tests ensure production reliability
+- **Type safety** - full type checking prevents runtime errors in job processing
+- **Clean separation** - API and worker processes use same codebase with different entry points
+- **Queue monitoring** - Redis CLI integration for real-time queue activity monitoring
+- **Comprehensive documentation** - detailed monitoring guide with Redis pattern explanations
+
+**Development Benefits:**
+- **Zero workflow changes** - existing deployment/undeploy workflows work unchanged as background jobs
+- **Async/await native** - modern Python asyncio patterns throughout the implementation
+- **Event correlation preserved** - all existing workflow tracking and event sourcing continues to work
+- **Enhanced CLI tooling** - unified tenant commands with proper endpoint routing
+- **Database integrity** - proper foreign key constraint handling in tenant deletion
+
+#### Infrastructure Requirements
+- **Local**: Redis via docker-compose (already exists) ✅
+- **Production**: Upstash Redis on Fly.io (already configured) ✅
+- **Workers**: arq worker processes (new deployment target)
+- **Monitoring**: Job status dashboard (simple web interface)
+
+#### API Evolution
+```python
+# Before: Synchronous (blocks for 60+ seconds)
+POST /tenant/{id}/deploy → {status: "active", machine_id: "..."}
+
+# After: Asynchronous (returns immediately)
+POST /tenant/{id}/deploy → {job_id: "uuid", workflow_id: "uuid", status: "queued"}
+GET  /jobs/{job_id}/status → {status: "running", progress: "deploying_machine", workflow_id: "uuid"}
+GET  /workflows/{workflow_id}/events → [...] # Existing event tracking works unchanged
+```
+
+**Technology Choice**: **arq (Redis)** over pgqueuer
+- **Existing Redis infrastructure** - Upstash + docker-compose already configured
+- **Better ecosystem** - monitoring tools, documentation, community
+- **Made by pydantic team** - aligns with existing Python stack
+- **Hybrid approach** - Redis for queue operations + Postgres for workflow state
+
+#### Job Uniqueness Implementation
+
+**Problem**: Multiple concurrent deployment requests for the same tenant could create duplicate jobs, wasting resources and potentially causing conflicts.
+
+**Solution**: Leverage ARQ's built-in job uniqueness feature using predictable job IDs:
+
+```python
+# JobQueueService implementation
+async def enqueue_deploy_job(self, tenant_id: UUID, image_tag: str | None = None) -> str:
+    unique_job_id = f"deploy-{tenant_id}"
+
+    job = await self.redis_pool.enqueue_job(
+        "deploy_tenant_job",
+        str(tenant_id),
+        image_tag,
+        _job_id=unique_job_id,  # ARQ prevents duplicates
+    )
+
+    if job is None:
+        # Job already exists - return existing job ID
+        return unique_job_id
+    else:
+        # New job created - return ARQ job ID
+        return job.job_id
+```
+
+**Key Features:**
+- **Predictable Job IDs**: `deploy-{tenant_id}`, `undeploy-{tenant_id}`
+- **Duplicate Prevention**: ARQ returns `None` for duplicate job IDs
+- **Graceful Handling**: Return existing job ID instead of raising errors
+- **Idempotent Operations**: Safe to retry deployment requests
+- **Clear Logging**: Distinguish "Enqueued new" vs "Found existing" jobs
+
+**Benefits:**
+- Prevents resource waste from duplicate deployments
+- Eliminates race conditions from concurrent requests
+- Makes job monitoring more predictable with consistent IDs
+- Provides natural deduplication without complex locking mechanisms
+
+
+## Notes
+
+### Design Philosophy Lessons
+- **Simplicity beats framework magic** - removing DBOS made the system more reliable and debuggable
+- **Event sourcing > complex orchestration** - database-backed event tracking provides better observability than framework abstractions
+- **Idempotent operations > resumable workflows** - each step handling its own retry logic is simpler than framework-managed resumability
+- **Explicit error handling > framework exception handling** - Python exceptions are clearer than orchestration framework error states
+
+### Future Considerations
+- **Monitoring integration** - workflow tracking events could feed into observability systems
+- **Performance optimization** - event querying patterns may benefit from additional indexing
+- **Audit compliance** - complete event trail supports regulatory requirements
+- **Operational dashboards** - workflow status could drive tenant health monitoring
+
+### Related Specifications
+- **SPEC-8**: TigrisFS Integration - bucket provisioning integrated with deployment workflow
+- **SPEC-1**: Specification-Driven Development Process - this spec follows the established format
+
+## Observations
+
+- [architecture] Removing framework complexity led to more maintainable system #simplification
+- [workflow] Single unified deployment workflow handles both provisioning and updates #consolidation
+- [observability] Event sourcing with workflow correlation provides complete audit trail #event-tracking
+- [database] Foreign key relationships between workflows and events enable powerful queries #schema-design
+- [testing] Integration tests with real infrastructure catch edge cases that unit tests miss #testing-strategy
+- [parameters] Consistent method signatures (workflow_id first) reduce cognitive overhead #api-design
+- [maintenance] Fewer workflows and dependencies reduce long-term maintenance burden #operational-excellence
+- [debugging] Plain Python exceptions are clearer than framework abstraction layers #developer-experience
+- [resilience] Exponential backoff retry patterns handle flaky external API calls gracefully #error-handling
+- [monitoring] Redis queue monitoring provides real-time operational visibility #observability
+- [ci-cd] Bulk update commands enable automated tenant deployments in continuous delivery pipelines #automation
+- [documentation] Comprehensive monitoring guides reduce operational learning curve #knowledge-management
+- [error-logging] Context-aware log levels (INFO for expected errors, ERROR for unexpected) improve signal-to-noise ratio #logging-strategy
+- [job-uniqueness] ARQ job uniqueness with predictable tenant-based IDs prevents duplicate operations and resource waste #deduplication
+
+## Implementation Notes
+
+### Configuration Integration
+- **Redis Configuration**: Add Redis settings to existing `apps/cloud/src/basic_memory_cloud/config.py`
+- **Local Development**: Leverage existing Redis setup from `docker-compose.yml`
+- **Production**: Use Upstash Redis configuration for production environments
+
+### Docker Entrypoint Strategy
+Create `entrypoint.sh` script to toggle between API server and worker processes using single Docker image:
+
+```bash
+#!/bin/bash
+
+# Entrypoint script for Basic Memory Cloud service
+# Supports multiple process types: api, worker
+
+set -e
+
+case "$1" in
+  "api")
+    echo "Starting Basic Memory Cloud API server..."
+    exec uvicorn basic_memory_cloud.main:app \
+      --host 0.0.0.0 \
+      --port 8000 \
+      --log-level info
+    ;;
+  "worker")
+    echo "Starting Basic Memory Cloud ARQ worker..."
+    # For ARQ worker implementation
+    exec python -m arq basic_memory_cloud.jobs.settings.WorkerSettings
+    ;;
+  *)
+    echo "Usage: $0 {api|worker}"
+    echo "  api    - Start the FastAPI server"
+    echo "  worker - Start the ARQ worker"
+    exit 1
+    ;;
+esac
+```
+
+### Fly.io Process Groups Configuration
+Use separate machine groups for API and worker processes with independent scaling:
+
+```toml
+# fly.toml app configuration for basic-memory-cloud
+app = 'basic-memory-cloud-dev-basic-machines'
+primary_region = 'dfw'
+org = 'basic-machines'
+kill_signal = 'SIGINT'
+kill_timeout = '5s'
+
+[build]
+
+# Process groups for API server and worker
+[processes]
+  api = "api"
+  worker = "worker"
+
+# Machine scaling configuration
+[[machine]]
+  size = 'shared-cpu-1x'
+  processes = ['api']
+  min_machines_running = 1
+  auto_stop_machines = false
+  auto_start_machines = true
+
+[[machine]]
+  size = 'shared-cpu-1x'
+  processes = ['worker']
+  min_machines_running = 1
+  auto_stop_machines = false
+  auto_start_machines = true
+
+[env]
+  # Python configuration
+  PYTHONUNBUFFERED = '1'
+  PYTHONPATH = '/app'
+
+  # Logging configuration
+  LOG_LEVEL = 'DEBUG'
+
+  # Redis configuration for ARQ
+  REDIS_URL = 'redis://basic-memory-cloud-redis.upstash.io'
+
+  # Database configuration
+  DATABASE_HOST = 'basic-memory-cloud-db-dev-basic-machines.internal'
+  DATABASE_PORT = '5432'
+  DATABASE_NAME = 'basic_memory_cloud'
+  DATABASE_USER = 'postgres'
+  DATABASE_SSL = 'true'
+
+  # Worker configuration
+  ARQ_MAX_JOBS = '10'
+  ARQ_KEEP_RESULT = '3600'
+
+  # Fly.io configuration
+  FLY_ORG = 'basic-machines'
+  FLY_REGION = 'dfw'
+
+# Internal service - no external HTTP exposure for worker
+# API accessible via basic-memory-cloud-dev-basic-machines.flycast:8000
+
+[[vm]]
+  size = 'shared-cpu-1x'
+```
+
+### Benefits of This Architecture
+- **Single Docker Image**: Both API and worker use same container with different entrypoints
+- **Independent Scaling**: Scale API and worker processes separately based on demand
+- **Clean Separation**: Web traffic handling separate from background job processing
+- **Existing Infrastructure**: Leverages current PostgreSQL + Redis setup without complexity
+- **Hybrid State Management**: Redis for queue operations, PostgreSQL for persistent workflow tracking
+
+## Relations
+
+- implements [[SPEC-8 TigrisFS Integration]]
+- follows [[SPEC-1 Specification-Driven Development Process]]
+- supersedes previous multi-workflow architecture

specs/SPEC-11 Basic Memory API Performance Optimization.md

@@ -31,8 +31,6 @@ HTTP requests to the API suffer from 350ms-2.6s latency overhead **before** any
 
 This creates compounding effects with tenant auto-start delays and increases timeout risk in cloud deployments.
 
-Github issue: https://github.com/basicmachines-co/basic-memory-cloud/issues/82
-
 ## What
 
 This optimization affects the **core basic-memory repository** components:
@@ -170,76 +168,19 @@ Validation Checklist
 - Documentation: Performance optimization documented in README
 - Cloud Integration: basic-memory-cloud sees performance benefits
 
-## Implementation Status ✅ COMPLETED
-
-**Implementation Date**: 2025-09-26
-**Branch**: `feature/spec-11-api-performance-optimization`
-**Commit**: `771f60b`
-
-### ✅ Phase 1: Database Connection Caching - IMPLEMENTED
-
-**Files Modified:**
-- `src/basic_memory/api/app.py` - Added database connection caching in app.state
-- `src/basic_memory/deps.py` - Updated get_engine_factory() to use cached connections
-- `src/basic_memory/config.py` - Added skip_initialization_sync configuration flag
-
-**Implementation Details:**
-1. **API Lifespan Caching**: Database engine and session_maker cached in app.state during startup
-2. **Dependency Injection Optimization**: get_engine_factory() now returns cached connections instead of calling get_or_create_db()
-3. **Project Reconciliation Removal**: Eliminated expensive reconcile_projects_with_config() from API startup
-4. **CLI Fallback Preserved**: Non-API contexts continue to work with fallback database initialization
-
-### ✅ Performance Validation - ACHIEVED
-
-**Live Testing Results** (2025-09-26 14:03-14:09):
-
-| Operation | Before | After | Improvement |
-|-----------|--------|-------|-------------|
-| `read_note` | 350ms-2.6s | **20ms** | **95-99% faster** |
-| `edit_note` | 350ms-2.6s | **218ms** | **75-92% faster** |
-| `search_notes` | 350ms-2.6s | **<500ms** | **Responsive** |
-| `list_memory_projects` | N/A | **<100ms** | **Fast** |
-
-**Key Achievements:**
-- ✅ **95-99% improvement** in read operations (primary workflow)
-- ✅ **75-92% improvement** in edit operations
-- ✅ **Zero overhead** for project switching
-- ✅ **Database connection overhead eliminated** (0ms vs 50-100ms)
-- ✅ **Project reconciliation delays removed** from API requests
-- ✅ **<500ms target achieved** for all operations except write (which includes file sync)
-
-### ✅ Backwards Compatibility - MAINTAINED
-
-- All existing functionality preserved
-- CLI operations unaffected
-- Fallback for non-API contexts maintained
-- No breaking changes to existing APIs
-- Optional configuration with safe defaults
-
-### ✅ Testing Validation - PASSED
-
-- Integration tests passing
-- Type checking clear
-- Linting checks passed
-- Live testing with real MCP tools successful
-- Multi-project workflows validated
-- Rapid project switching validated
-
-## Notes
+Notes
 
 Implementation Priority:
-- ✅ Phase 1 COMPLETED: Database connection caching provides 95%+ performance gains
-- ⚪ Phase 2 NOT NEEDED: Project reconciliation removal achieved the goals
-- ⚪ Phase 3 INCLUDED: skip_initialization_sync flag added
+- Phase 1 provides 80% of performance gains and should be implemented first
+- Phase 2 provides remaining 20% and addresses edge cases
+- Phase 3 is optional for maximum cloud optimization
 
 Risk Mitigation:
-- ✅ All changes backwards compatible implemented
-- ✅ Gradual implementation successful (Phase 1 → validation)
-- ✅ Easy rollback via configuration flags available
+- All changes backwards compatible
+- Gradual rollout possible (Phase 1 → 2 → 3)
+- Easy rollback via configuration flags
 
 Cloud Integration:
-- ✅ This optimization directly addresses basic-memory-cloud issue #82
-- ✅ Changes in core basic-memory will benefit all cloud tenants
-- ✅ No changes needed in basic-memory-cloud itself
-
-**Result**: SPEC-11 performance optimizations successfully implemented and validated. The 95-99% improvement in MCP tool response times exceeds the original 50-80% target, providing exceptional performance gains for cloud deployments and local usage.
+- This optimization directly addresses basic-memory-cloud issue #82
+- Changes in core basic-memory will benefit all cloud tenants
+- No changes needed in basic-memory-cloud itself

specs/SPEC-12 OpenTelemetry Observability.md

@@ -0,0 +1,182 @@
+# SPEC-12: OpenTelemetry Observability
+
+## Why
+
+We need comprehensive observability for basic-memory-cloud to:
+- Track request flows across our multi-tenant architecture (MCP → Cloud → API services)
+- Debug performance issues and errors in production
+- Understand user behavior and system usage patterns
+- Correlate issues to specific tenants for targeted debugging
+- Monitor service health and latency across the distributed system
+
+Currently, we only have basic logging without request correlation or distributed tracing capabilities.
+
+## What
+
+Implement OpenTelemetry instrumentation across all basic-memory-cloud services with:
+
+### Core Requirements
+1. **Distributed Tracing**: End-to-end request tracing from MCP gateway through to tenant API instances
+2. **Tenant Correlation**: All traces tagged with tenant_id, user_id, and workos_user_id
+3. **Service Identification**: Clear service naming and namespace separation
+4. **Auto-instrumentation**: Automatic tracing for FastAPI, SQLAlchemy, HTTP clients
+5. **Grafana Cloud Integration**: Direct OTLP export to Grafana Cloud Tempo
+
+### Services to Instrument
+- **MCP Gateway** (basic-memory-mcp): Entry point with JWT extraction
+- **Cloud Service** (basic-memory-cloud): Provisioning and management operations
+- **API Service** (basic-memory-api): Tenant-specific instances
+- **Worker Processes** (ARQ workers): Background job processing
+
+### Key Trace Attributes
+- `tenant.id`: UUID from UserProfile.tenant_id
+- `user.id`: WorkOS user identifier
+- `user.email`: User email for debugging
+- `service.name`: Specific service identifier
+- `service.namespace`: Environment (development/production)
+- `operation.type`: Business operation (provision/update/delete)
+- `tenant.app_name`: Fly.io app name for tenant instances
+
+## How
+
+### Phase 1: Setup OpenTelemetry SDK
+1. Add OpenTelemetry dependencies to each service's pyproject.toml:
+   ```python
+   "opentelemetry-distro[otlp]>=1.29.0",
+   "opentelemetry-instrumentation-fastapi>=0.50b0",
+   "opentelemetry-instrumentation-httpx>=0.50b0",
+   "opentelemetry-instrumentation-sqlalchemy>=0.50b0",
+   "opentelemetry-instrumentation-logging>=0.50b0",
+   ```
+
+2. Create shared telemetry initialization module (`apps/shared/telemetry.py`)
+
+3. Configure Grafana Cloud OTLP endpoint via environment variables:
+   ```bash
+   OTEL_EXPORTER_OTLP_ENDPOINT=https://otlp-gateway-prod-us-east-2.grafana.net/otlp
+   OTEL_EXPORTER_OTLP_HEADERS=Authorization=Basic[token]
+   OTEL_EXPORTER_OTLP_PROTOCOL=http/protobuf
+   ```
+
+### Phase 2: Instrument MCP Gateway
+1. Extract tenant context from AuthKit JWT in middleware
+2. Create root span with tenant attributes
+3. Propagate trace context to downstream services via headers
+
+### Phase 3: Instrument Cloud Service
+1. Continue trace from MCP gateway
+2. Add operation-specific attributes (provisioning events)
+3. Instrument ARQ worker jobs for async operations
+4. Track Fly.io API calls and latency
+
+### Phase 4: Instrument API Service
+1. Extract tenant context from JWT
+2. Add machine-specific metadata (instance ID, region)
+3. Instrument database operations with SQLAlchemy
+4. Track MCP protocol operations
+
+### Phase 5: Configure and Deploy
+1. Add OTLP configuration to `.env.example` and `.env.example.secrets`
+2. Set Fly.io secrets for production deployment
+3. Update Dockerfiles to use `opentelemetry-instrument` wrapper
+4. Deploy to development environment first for testing
+
+## How to Evaluate
+
+### Success Criteria
+1. **End-to-end traces visible in Grafana Cloud** showing complete request flow
+2. **Tenant filtering works** - Can filter traces by tenant_id to see all requests for a user
+3. **Service maps accurate** - Grafana shows correct service dependencies
+4. **Performance overhead < 5%** - Minimal latency impact from instrumentation
+5. **Error correlation** - Can trace errors back to specific tenant and operation
+
+### Testing Checklist
+- [x] Single request creates connected trace across all services
+- [x] Tenant attributes present on all spans
+- [x] Background jobs (ARQ) appear in traces
+- [x] Database queries show in trace timeline
+- [x] HTTP calls to Fly.io API tracked
+- [x] Traces exported successfully to Grafana Cloud
+- [x] Can search traces by tenant_id in Grafana
+- [x] Service dependency graph shows correct flow
+
+### Monitoring Success
+- All services reporting traces to Grafana Cloud
+- No OTLP export errors in logs
+- Trace sampling working correctly (if implemented)
+- Resource usage acceptable (CPU/memory)
+
+## Dependencies
+- Grafana Cloud account with OTLP endpoint configured
+- OpenTelemetry Python SDK v1.29.0+
+- FastAPI instrumentation compatibility
+- Network access from Fly.io to Grafana Cloud
+
+## Implementation Assignment
+**Recommended Agent**: python-developer
+- Requires Python/FastAPI expertise
+- Needs understanding of distributed systems
+- Must implement middleware and context propagation
+- Should understand OpenTelemetry SDK and instrumentation
+
+## Follow-up Tasks
+
+### Enhanced Log Correlation
+While basic trace-to-log correlation works automatically via OpenTelemetry logging instrumentation, consider adding structured logging for improved log filtering:
+
+1. **Structured Logging Context**: Add `logger.bind()` calls to inject tenant/user context directly into log records
+2. **Custom Loguru Formatter**: Extract OpenTelemetry span attributes for better log readability
+3. **Direct Log Filtering**: Enable searching logs directly by tenant_id, workflow_id without going through traces
+
+This would complement the existing automatic trace correlation and provide better log search capabilities.
+
+## Alternative Solution: Logfire
+
+After implementing OpenTelemetry with Grafana Cloud, we discovered limitations in the observability experience:
+- Traces work but lack useful context without correlated logs
+- Setting up log correlation with Grafana is complex and requires additional infrastructure
+- The developer experience for Python observability is suboptimal
+
+### Logfire Evaluation
+
+**Pydantic Logfire** offers a compelling alternative that addresses your specific requirements:
+
+#### Core Requirements Match
+- ✅ **User Activity Tracking**: Automatic request tracing with business context
+- ✅ **Error Monitoring**: Built-in exception tracking with full context
+- ✅ **Performance Metrics**: Automatic latency and performance monitoring
+- ✅ **Request Tracing**: Native distributed tracing across services
+- ✅ **Log Correlation**: Seamless trace-to-log correlation without setup
+
+#### Key Advantages
+1. **Python-First Design**: Built specifically for Python/FastAPI applications by the Pydantic team
+2. **Simple Integration**: `pip install logfire` + `logfire.configure()` vs complex OTLP setup
+3. **Automatic Correlation**: Logs automatically include trace context without manual configuration
+4. **Real-time SQL Interface**: Query spans and logs using SQL with auto-completion
+5. **Better Developer UX**: Purpose-built observability UI vs generic Grafana dashboards
+6. **Loguru Integration**: `logger.configure(handlers=[logfire.loguru_handler()])` maintains existing logging
+
+#### Pricing Assessment
+- **Free Tier**: 10M spans/month (suitable for development and small production workloads)
+- **Transparent Pricing**: $1 per million spans/metrics after free tier
+- **No Hidden Costs**: No per-host fees, only usage-based metering
+- **Production Ready**: Recently exited beta, enterprise features available
+
+#### Migration Path
+The existing OpenTelemetry instrumentation is compatible - Logfire uses OpenTelemetry under the hood, so the current spans and attributes would work unchanged.
+
+### Recommendation
+
+**Consider migrating to Logfire** for the following reasons:
+1. It directly addresses the "next to useless" traces problem by providing integrated logs
+2. Dramatically simpler setup and maintenance compared to Grafana Cloud + custom log correlation
+3. Better ROI on observability investment with purpose-built Python tooling
+4. Free tier sufficient for current development needs with clear scaling path
+
+The current Grafana Cloud implementation provides a solid foundation and could remain as a backup/export target, while Logfire becomes the primary observability platform.
+
+## Status
+**Created**: 2024-01-28
+**Status**: Completed (OpenTelemetry + Grafana Cloud)
+**Next Phase**: Evaluate Logfire migration
+**Priority**: High - Critical for production observability

specs/SPEC-13 CLI Authentication with Subscription Validation.md

@@ -340,398 +340,6 @@ This architecture makes the fix comprehensive and maintainable.
 - Want to reduce database dependency
 - Scale requires fewer database queries
 
-## Post-Deployment Test Plan
-
-This test plan should be executed after deploying the cloud service to verify subscription validation works end-to-end.
-
-### Prerequisites
-
-Before testing, ensure you have:
-- [ ] Cloud service deployed with Phase 1 changes
-- [ ] CLI installed with Phase 2 changes (`basic-memory` from local dev)
-- [ ] Access to database to check/modify subscription status
-- [ ] Two test user accounts:
-  - User A: No subscription (fresh WorkOS signup)
-  - User B: Active subscription (via Polar or manual DB insert)
-
-### Test Execution
-
-#### Test 1: User Without Subscription (Blocked Access) ❌
-
-**Setup:**
-1. Create fresh WorkOS account (User A) via AuthKit
-2. Verify in database: No subscription record exists for User A's `workos_user_id`
-
-**Test Steps:**
-```bash
-# Step 1: Attempt login
-bm cloud login
-```
-
-**Expected Results:**
-- ✅ OAuth flow completes successfully
-- ✅ JWT token obtained and stored in `~/.basic-memory/auth/token`
-- ❌ Login fails with "Subscription Required" error
-- ✅ Error message displays:
-  - "✗ Subscription Required"
-  - "Active subscription required for CLI access"
-  - Subscribe URL: "https://basicmemory.com/subscribe"
-  - Instructions to run `bm cloud login` after subscribing
-- ❌ Cloud mode NOT enabled (check with `bm cloud status`)
-
-**Test Steps (continued):**
-```bash
-# Step 2: Attempt to access cloud features
-bm cloud status
-
-# Step 3: Try direct API call
-curl -H "Authorization: Bearer <token>" https://<cloud-host>/proxy/health
-```
-
-**Expected Results:**
-- ✅ `bm cloud status` shows "Mode: Local (disabled)"
-- ✅ Direct API call returns 403 with subscription_required error
-
-**Database Verification:**
-```sql
--- Verify no subscription exists
-SELECT * FROM subscriptions
-WHERE workos_user_id = '<user-a-workos-id>';
--- Should return 0 rows
-```
-
----
-
-#### Test 2: User With Active Subscription (Full Access) ✅
-
-**Setup:**
-1. Use User B with active subscription
-2. Verify in database: Subscription exists with `status = 'active'` and `current_period_end > NOW()`
-
-**Database Verification:**
-```sql
--- Verify active subscription exists
-SELECT workos_user_id, status, current_period_end
-FROM subscriptions
-WHERE workos_user_id = '<user-b-workos-id>';
--- Should show: status='active', current_period_end in future
-```
-
-**Test Steps:**
-```bash
-# Step 1: Login
-bm cloud login
-
-# Step 2: Check cloud mode
-bm cloud status
-
-# Step 3: Setup bisync
-bm cloud setup
-
-# Step 4: Test MCP tools via proxy
-curl -H "Authorization: Bearer <token>" \
-  https://<cloud-host>/proxy/<project-name>/health
-
-# Step 5: List projects
-bm project list
-
-# Step 6: Create a test note
-bm tool write-note \
-  --title "Test Note" \
-  --folder "test-project" \
-  --content "Testing subscription validation"
-```
-
-**Expected Results:**
-- ✅ Login succeeds without errors
-- ✅ Cloud mode enabled: "Mode: Cloud (enabled)"
-- ✅ Cloud instance health check succeeds
-- ✅ Bisync setup completes successfully
-- ✅ Direct API calls succeed (200 OK)
-- ✅ Projects list successfully
-- ✅ Note creation succeeds
-
----
-
-#### Test 3: Subscription Expiration (Access Revoked) 🔄
-
-**Setup:**
-1. Use User B (currently has active subscription and cloud mode enabled)
-2. User should be able to access cloud features initially
-
-**Test Steps:**
-```bash
-# Step 1: Verify current access works
-bm cloud status
-# Should show "Cloud (enabled)" and healthy instance
-
-# Step 2: Expire subscription in database
-# (See SQL below)
-
-# Step 3: Attempt to access cloud features
-bm cloud status
-
-# Step 4: Try to login again
-bm cloud logout
-bm cloud login
-```
-
-**Database Operations:**
-```sql
--- Expire the subscription
-UPDATE subscriptions
-SET status = 'cancelled',
-    current_period_end = NOW() - INTERVAL '1 day'
-WHERE workos_user_id = '<user-b-workos-id>';
-
--- Verify expiration
-SELECT workos_user_id, status, current_period_end
-FROM subscriptions
-WHERE workos_user_id = '<user-b-workos-id>';
--- Should show: status='cancelled', current_period_end in past
-```
-
-**Expected Results:**
-- ❌ `bm cloud status` fails with 403 subscription_required error
-- ❌ Re-login fails with "Subscription Required" error
-- ✅ Error includes subscribe URL
-
----
-
-#### Test 4: Subscription Renewal (Access Restored) ✅
-
-**Setup:**
-1. Continue from Test 3 (User B with expired subscription)
-
-**Test Steps:**
-```bash
-# Step 1: Renew subscription in database
-# (See SQL below)
-
-# Step 2: Login again
-bm cloud login
-
-# Step 3: Verify access restored
-bm cloud status
-
-# Step 4: Test project access
-bm project list
-```
-
-**Database Operations:**
-```sql
--- Renew the subscription
-UPDATE subscriptions
-SET status = 'active',
-    current_period_end = NOW() + INTERVAL '30 days'
-WHERE workos_user_id = '<user-b-workos-id>';
-
--- Verify renewal
-SELECT workos_user_id, status, current_period_end
-FROM subscriptions
-WHERE workos_user_id = '<user-b-workos-id>';
--- Should show: status='active', current_period_end 30 days in future
-```
-
-**Expected Results:**
-- ✅ Login succeeds
-- ✅ Cloud mode enabled
-- ✅ Cloud status shows healthy
-- ✅ Projects list successfully
-- ✅ **Access immediately restored** (no delay)
-
----
-
-#### Test 5: Endpoint Coverage (All Protected Endpoints) 🔐
-
-**Setup:**
-1. Use User A (no subscription) to test blocked access
-2. Use User B (active subscription) to test allowed access
-
-**Test Matrix:**
-
-| Endpoint | Method | User A (No Sub) | User B (Active Sub) |
-|----------|--------|----------------|---------------------|
-| `/proxy/health` | GET | 403 ❌ | 200 ✅ |
-| `/proxy/<project>/health` | GET | 403 ❌ | 200 ✅ |
-| `/proxy/<project>/search` | POST | 403 ❌ | 200 ✅ |
-| `/tenant/mount/info` | GET | 403 ❌ | 200 ✅ |
-| `/tenant/mount/credentials` | POST | 403 ❌ | 200 ✅ |
-
-**Test Commands:**
-```bash
-# Get tokens for both users
-TOKEN_A="<user-a-token>"
-TOKEN_B="<user-b-token>"
-
-# Test /proxy/health
-curl -H "Authorization: Bearer $TOKEN_A" \
-  https://<cloud-host>/proxy/health
-# Expected: 403 with subscription_required
-
-curl -H "Authorization: Bearer $TOKEN_B" \
-  https://<cloud-host>/proxy/health
-# Expected: 200 OK
-
-# Test /tenant/mount/info
-curl -H "Authorization: Bearer $TOKEN_A" \
-  https://<cloud-host>/tenant/mount/info
-# Expected: 403 with subscription_required
-
-curl -H "Authorization: Bearer $TOKEN_B" \
-  https://<cloud-host>/tenant/mount/info
-# Expected: 200 OK with mount info
-
-# Test /proxy/<project>/health
-curl -H "Authorization: Bearer $TOKEN_B" \
-  https://<cloud-host>/proxy/<project-name>/health
-# Expected: 200 OK
-```
-
----
-
-#### Test 6: Error Response Format Validation 📋
-
-**Test Steps:**
-```bash
-# Get 403 response for user without subscription
-curl -i -H "Authorization: Bearer $TOKEN_A" \
-  https://<cloud-host>/proxy/health
-```
-
-**Expected Response Format:**
-```http
-HTTP/1.1 403 Forbidden
-Content-Type: application/json
-
-{
-  "error": "subscription_required",
-  "message": "Active subscription required for CLI access",
-  "subscribe_url": "https://basicmemory.com/subscribe"
-}
-```
-
-**Validation Checklist:**
-- ✅ Status code is exactly 403
-- ✅ Response is valid JSON
-- ✅ `error` field equals "subscription_required"
-- ✅ `message` field is present and informative
-- ✅ `subscribe_url` field is present and valid URL
-
----
-
-#### Test 7: Admin Access Bypass 👑
-
-**Purpose:** Verify admin users can still access admin endpoints without subscription
-
-**Setup:**
-1. Use admin user account (member of admin organization in WorkOS)
-
-**Test Steps:**
-```bash
-# Login as admin
-python -m basic_memory_cloud.cli.tenant_cli login
-
-# List tenants (admin-only endpoint)
-python -m basic_memory_cloud.cli.tenant_cli list-tenants
-
-# Create tenant (admin-only endpoint)
-python -m basic_memory_cloud.cli.tenant_cli create-tenant \
-  --workos-user-id <test-user-id>
-```
-
-**Expected Results:**
-- ✅ Admin login succeeds
-- ✅ Admin can access `/tenants/*` endpoints
-- ✅ Admin operations work regardless of subscription status
-- ✅ Admin endpoints use `AdminUserHybridDep` (not affected by subscription check)
-
----
-
-### Test Results Template
-
-Copy this template to track your test execution:
-
-```markdown
-## SPEC-13 Test Execution - [Date]
-
-### Environment
-- Cloud Service: [URL]
-- Cloud Service Version: [commit/tag]
-- CLI Version: [commit/tag]
-- Database: [production/staging]
-
-### Test Results
-
-#### Test 1: User Without Subscription ❌
-- [ ] OAuth flow succeeds
-- [ ] Subscription error displayed
-- [ ] Subscribe URL shown
-- [ ] Cloud mode NOT enabled
-- [ ] Direct API call blocked
-
-**Issues:** [None / List issues]
-
-#### Test 2: User With Active Subscription ✅
-- [ ] Login succeeds
-- [ ] Cloud mode enabled
-- [ ] Health check passes
-- [ ] Bisync setup works
-- [ ] MCP tools work
-- [ ] Projects accessible
-
-**Issues:** [None / List issues]
-
-#### Test 3: Subscription Expiration 🔄
-- [ ] Active user can access initially
-- [ ] After expiration, access blocked
-- [ ] Error message clear
-- [ ] Cloud status fails appropriately
-
-**Issues:** [None / List issues]
-
-#### Test 4: Subscription Renewal ✅
-- [ ] Renewed subscription in DB
-- [ ] Login succeeds immediately
-- [ ] Access fully restored
-- [ ] No caching delays
-
-**Issues:** [None / List issues]
-
-#### Test 5: Endpoint Coverage 🔐
-- [ ] All proxy endpoints protected
-- [ ] All mount endpoints protected
-- [ ] Subscription check consistent
-- [ ] Error responses correct
-
-**Issues:** [None / List issues]
-
-#### Test 6: Error Response Format 📋
-- [ ] 403 status code
-- [ ] Valid JSON response
-- [ ] All required fields present
-- [ ] Subscribe URL valid
-
-**Issues:** [None / List issues]
-
-#### Test 7: Admin Access Bypass 👑
-- [ ] Admin login works
-- [ ] Admin endpoints accessible
-- [ ] No subscription requirement
-
-**Issues:** [None / List issues]
-
-### Overall Result
-- [ ] All tests passed
-- [ ] Ready for production
-
-**Summary:** [Brief summary of test execution]
-
-**Sign-off:** [Your name/date]
-```
-
----
-
 ## How to Evaluate
 
 ### Success Criteria
@@ -1065,35 +673,35 @@ The extra HTTP hop is minimal (< 10ms) and worth it for architectural benefits.
   - [ ] Call `/tenant/mount/info` with valid JWT and active subscription → expect 200
   - [ ] Verify error response structure matches spec
 
-### Phase 2: CLI (basic-memory) ✅
+### Phase 2: CLI (basic-memory)
 
-#### Task 2.1: Review and understand CLI authentication flow ✅
+#### Task 2.1: Review and understand CLI authentication flow
 **Files**: `src/basic_memory/cli/commands/cloud/`
 
-- [x] Read `core_commands.py` to understand current login flow
-- [x] Read `api_client.py` to understand current error handling
-- [x] Identify where 403 errors should be caught
-- [x] Identify what error messages should be displayed
-- [x] Document current behavior in spec if needed
+- [ ] Read `core_commands.py` to understand current login flow
+- [ ] Read `api_client.py` to understand current error handling
+- [ ] Identify where 403 errors should be caught
+- [ ] Identify what error messages should be displayed
+- [ ] Document current behavior in spec if needed
 
-#### Task 2.2: Update API client error handling ✅
+#### Task 2.2: Update API client error handling
 **File**: `src/basic_memory/cli/commands/cloud/api_client.py`
 
-- [x] Add custom exception class `SubscriptionRequiredError` (or similar)
-- [x] Update HTTP error handling to parse 403 responses
-- [x] Extract `error`, `message`, and `subscribe_url` from error detail
-- [x] Raise specific exception for subscription_required errors
-- [x] Run `just typecheck` in basic-memory repo to verify types
+- [ ] Add custom exception class `SubscriptionRequiredError` (or similar)
+- [ ] Update HTTP error handling to parse 403 responses
+- [ ] Extract `error`, `message`, and `subscribe_url` from error detail
+- [ ] Raise specific exception for subscription_required errors
+- [ ] Run `just typecheck` in basic-memory repo to verify types
 
-#### Task 2.3: Update CLI login command error handling ✅
+#### Task 2.3: Update CLI login command error handling
 **File**: `src/basic_memory/cli/commands/cloud/core_commands.py`
 
-- [x] Import the subscription error exception
-- [x] Wrap login flow with try/except for subscription errors
-- [x] Display user-friendly error message with rich console
-- [x] Show subscribe URL prominently
-- [x] Provide actionable next steps
-- [x] Run `just typecheck` to verify types
+- [ ] Import the subscription error exception
+- [ ] Wrap login flow with try/except for subscription errors
+- [ ] Display user-friendly error message with rich console
+- [ ] Show subscribe URL prominently
+- [ ] Provide actionable next steps
+- [ ] Run `just typecheck` to verify types
 
 **Expected error handling**:
 ```python
@@ -1111,33 +719,30 @@ except SubscriptionRequiredError as e:
     raise typer.Exit(1)
 ```
 
-#### Task 2.4: Update CLI tests ✅
-**File**: `tests/cli/test_cloud_authentication.py` (created)
+#### Task 2.4: Update CLI tests
+**File**: `tests/cli/test_cloud_commands.py`
 
-- [x] Add test: `test_login_without_subscription_shows_error()`
+- [ ] Add test: `test_login_without_subscription_shows_error()`
   - Mock 403 subscription_required response
   - Call login command
   - Assert error message displayed
   - Assert subscribe URL shown
-- [x] Add test: `test_login_with_subscription_succeeds()`
+- [ ] Add test: `test_login_with_subscription_succeeds()`
   - Mock successful authentication + subscription check
   - Call login command
   - Assert success message
-- [x] Add test: `test_parse_subscription_required_error()` (API client error parsing)
-- [x] Add test: `test_parse_generic_403_error()` (generic 403 handling)
-- [x] Add test: `test_login_authentication_failure()` (auth failure handling)
-- [x] Run `uv run pytest` to verify tests pass (5/5 passed)
+- [ ] Run `just test` to verify tests pass
 
-#### Task 2.5: Update CLI documentation ✅
-**File**: `docs/cloud-cli.md`
+#### Task 2.5: Update CLI documentation
+**File**: `docs/cloud-cli.md` (in basic-memory-docs repo)
 
-- [x] Add "Prerequisites" section if not present
-- [x] Document subscription requirement
-- [x] Add "Troubleshooting" section
-- [x] Document "Subscription Required" error
-- [x] Provide subscribe URL
-- [x] Add FAQ entry about subscription errors
-- [x] Build docs locally to verify formatting
+- [ ] Add "Prerequisites" section if not present
+- [ ] Document subscription requirement
+- [ ] Add "Troubleshooting" section
+- [ ] Document "Subscription Required" error
+- [ ] Provide subscribe URL
+- [ ] Add FAQ entry about subscription errors
+- [ ] Build docs locally to verify formatting
 
 ### Phase 3: End-to-End Testing
 
@@ -1227,12 +832,12 @@ Use this high-level checklist to track overall progress:
 - [ ] Add integration tests for dependency
 - [ ] Deploy and verify cloud service
 
-### Phase 2: CLI Updates ✅
-- [x] Review CLI authentication flow
-- [x] Update API client error handling
-- [x] Update CLI login command error handling
-- [x] Add CLI tests
-- [x] Update CLI documentation
+### Phase 2: CLI Updates 🔄
+- [ ] Review CLI authentication flow
+- [ ] Update API client error handling
+- [ ] Update CLI login command error handling
+- [ ] Add CLI tests
+- [ ] Update CLI documentation
 
 ### Phase 3: End-to-End Testing 🧪
 - [ ] Create test user accounts
@@ -1310,118 +915,3 @@ Use this high-level checklist to track overall progress:
 - This spec prioritizes security over convenience - better to block unauthorized access than risk revenue loss
 - Clear error messages are critical - users should understand why they're blocked and how to resolve it
 - Consider adding telemetry to track subscription_required errors for monitoring signup conversion
-
-## Implementation Log
-
-### Phase 2 Completion - 2025-10-03
-
-Phase 2 (CLI Updates) completed successfully with the following implementation:
-
-**Files Modified:**
-- `src/basic_memory/cli/commands/cloud/api_client.py` - Added `SubscriptionRequiredError` exception and enhanced error handling
-- `src/basic_memory/cli/commands/cloud/core_commands.py` - Updated login command to verify subscription access
-- `docs/cloud-cli.md` - Added Prerequisites and Subscription Issues sections
-
-**Files Created:**
-- `tests/cli/test_cloud_authentication.py` - Comprehensive test coverage (6 tests, all passing)
-
-**Key Implementation Details:**
-- `SubscriptionRequiredError` exception with `subscribe_url` field for user guidance
-- Enhanced `CloudAPIError` to include `status_code` and `detail` fields
-- Login flow now calls `/proxy/health` to verify subscription before enabling cloud mode
-- User-friendly error messages with direct subscribe link
-- 100% test coverage of new error handling paths
-
-**Test Results:**
-- All 6 tests passing
-- Type checking: 0 errors, 0 warnings
-- Linting: All checks passed
-
-**Next Steps:**
-- Phase 3: End-to-End Testing (manual testing with real users, subscription state transitions)
-- Phase 1: Complete remaining cloud service tests (unit tests, integration tests, deployment verification)
-
----
-
-### End-to-End Test Execution - 2025-10-03
-
-**Environment:**
-- Cloud Service: https://cloud.basicmemory.com
-- Cloud Service Version: Phase 1 deployed (with subscription validation)
-- CLI Version: Phase 2 implementation (local dev build)
-- Database: Production
-
-**Test Results:**
-
-#### Test 1: User Without Subscription ✅ PASSED
-- [x] OAuth flow succeeds
-- [x] Subscription error displayed
-- [x] Subscribe URL shown
-- [x] Cloud mode NOT enabled
-- [x] Clean error output (no traceback)
-
-**Output:**
-```
-✅ Successfully authenticated with WorkOS!
-Verifying subscription access...
-
-✗ Subscription Required
-
-Active subscription required
-
-Subscribe at: https://basicmemory.com/subscribe
-
-Once you have an active subscription, run bm cloud login again.
-```
-
-**Issues:** None
-
----
-
-#### Test 2: User With Active Subscription ✅ PASSED
-- [x] Login succeeds
-- [x] Cloud mode enabled
-- [x] Clean success message
-- [x] Ready for cloud operations
-
-**Output:**
-```
-✅ Successfully authenticated with WorkOS!
-Verifying subscription access...
-✓ Cloud mode enabled
-All CLI commands now work against https://cloud.basicmemory.com
-```
-
-**Issues:** None
-
----
-
-**Additional Implementation Notes:**
-
-**API Response Format Compatibility:**
-- Cloud service returns errors in FastAPI HTTPException format (nested under `"detail"` key)
-- CLI correctly handles both nested and flat response formats
-- Error parsing logic:
-  ```python
-  detail_obj = error_detail.get("detail", error_detail)
-  if isinstance(detail_obj, dict) and detail_obj.get("error") == "subscription_required":
-      # Handle subscription error
-  ```
-
-**Updated Test Coverage:**
-- Added `test_parse_subscription_required_error_flat_format()` for backward compatibility
-- Total: 6 tests, all passing
-- Files updated:
-  - `src/basic_memory/cli/commands/cloud/api_client.py` - Support both response formats
-  - `tests/cli/test_cloud_authentication.py` - Added flat format test
-
-**Overall Result:**
-- [x] Core authentication flows validated
-- [x] Error handling working as designed
-- [x] User experience is clean and helpful
-- [x] Ready for production use
-
-**Summary:**
-SPEC-13 Phase 2 successfully validated in production environment. Both unauthorized and authorized user flows work correctly. The subscription validation is functioning end-to-end with clear, user-friendly error messages and seamless success path. No issues discovered during testing.
-
-**Sign-off:** Phase 2 Complete - 2025-10-03

specs/SPEC-14 Cloud Git Versioning & GitHub Backup.md

@@ -0,0 +1,210 @@
+---
+title: 'SPEC-14: Cloud Git Versioning & GitHub Backup'
+type: spec
+permalink: specs/spec-14-cloud-git-versioning
+tags:
+- git
+- github
+- backup
+- versioning
+- cloud
+related:
+- specs/spec-9-multi-project-bisync
+- specs/spec-9-follow-ups-conflict-sync-and-observability
+status: deferred
+---
+
+# SPEC-14: Cloud Git Versioning & GitHub Backup
+
+**Status: DEFERRED** - Postponed until multi-user/teams feature development. Using S3 versioning (SPEC-9.1) for v1 instead.
+
+## Why Deferred
+
+**Original goals can be met with simpler solutions:**
+- Version history → **S3 bucket versioning** (automatic, zero config)
+- Offsite backup → **Tigris global replication** (built-in)
+- Restore capability → **S3 version restore** (`bm cloud restore --version-id`)
+- Collaboration → **Deferred to teams/multi-user feature** (not v1 requirement)
+
+**Complexity vs value trade-off:**
+- Git integration adds: committer service, puller service, webhooks, LFS, merge conflicts
+- Risk: Loop detection between Git ↔ rclone bisync ↔ local edits
+- S3 versioning gives 80% of value with 5% of complexity
+
+**When to revisit:**
+- Teams/multi-user features (PR-based collaboration workflow)
+- User requests for commit messages and branch-based workflows
+- Need for fine-grained audit trail beyond S3 object metadata
+
+---
+
+## Original Specification (for reference)
+
+## Why
+Early access users want **transparent version history**, easy **offsite backup**, and a familiar **restore/branching** workflow. Git/GitHub integration would provide:
+- Auditable history of every change (who/when/why)
+- Branches/PRs for review and collaboration
+- Offsite private backup under the user's control
+- Escape hatch: users can always `git clone` their knowledge base
+
+**Note:** These goals are now addressed via S3 versioning (SPEC-9.1) for single-user use case.
+
+## Goals
+- **Transparent**: Users keep using Basic Memory; Git runs behind the scenes.
+- **Private**: Push to a **private GitHub repo** that the user owns (or tenant org).
+- **Reliable**: No data loss, deterministic mapping of filesystem ↔ Git.
+- **Composable**: Plays nicely with SPEC‑9 bisync and upcoming conflict features (SPEC‑9 Follow‑Ups).
+
+**Non‑Goals (for v1):**
+- Fine‑grained per‑file encryption in Git history (can be layered later).
+- Large media optimization beyond Git LFS defaults.
+
+## User Stories
+1. *As a user*, I connect my GitHub and choose a private backup repo.
+2. *As a user*, every change I make in cloud (or via bisync) is **committed** and **pushed** automatically.
+3. *As a user*, I can **restore** a file/folder/project to a prior version.
+4. *As a power user*, I can **git pull/push** directly to collaborate outside the app.
+5. *As an admin*, I can enforce repo ownership (tenant org) and least‑privilege scopes.
+
+## Scope
+- **In scope:** Full repo backup of `/app/data/` (all projects) with optional selective subpaths.
+- **Out of scope (v1):** Partial shallow mirrors; encrypted Git; cross‑provider SCM (GitLab/Bitbucket).
+
+## Architecture
+### Topology
+- **Authoritative working tree**: `/app/data/` (bucket mount) remains the source of truth (SPEC‑9).
+- **Bare repo** lives alongside: `/app/git/${tenant}/knowledge.git` (server‑side).
+- **Mirror remote**: `github.com/<owner>/<repo>.git` (private).
+
+```mermaid
+flowchart LR
+  A[/Users & Agents/] -->|writes/edits| B[/app/data/]
+  B -->|file events| C[Committer Service]
+  C -->|git commit| D[(Bare Repo)]
+  D -->|push| E[(GitHub Private Repo)]
+  E -->|webhook (push)| F[Puller Service]
+  F -->|git pull/merge| D
+  D -->|checkout/merge| B
+```
+
+### Services
+- **Committer Service** (daemon):
+  - Watches `/app/data/` for changes (inotify/poll)
+  - Batches changes (debounce e.g. 2–5s)
+  - Writes `.bmmeta` (if present) into commit message trailer (see Follow‑Ups)
+  - `git add -A && git commit -m "chore(sync): <summary>
+
+BM-Meta: <json>"`
+  - Periodic `git push` to GitHub mirror (configurable interval)
+- **Puller Service** (webhook target):
+  - Receives GitHub webhook (push) → `git fetch`
+  - **Fast‑forward** merges to `main` only; reject non‑FF unless policy allows
+  - Applies changes back to `/app/data/` via clean checkout
+  - Emits sync events for Basic Memory indexers
+
+### Auth & Security
+- **GitHub App** (recommended): minimal scopes: `contents:read/write`, `metadata:read`, webhook.
+- Tenant‑scoped installation; repo created in user account or tenant org.
+- Tokens stored in KMS/secret manager; rotated automatically.
+- Optional policy: allow only **FF merges** on `main`; non‑FF requires PR.
+
+### Repo Layout
+- **Monorepo** (default): one repo per tenant mirrors `/app/data/` with subfolders per project.
+- Optional multi‑repo mode (later): one repo per project.
+
+### File Handling
+- Honor `.gitignore` generated from `.bmignore.rclone` + BM defaults (cache, temp, state).
+- **Git LFS** for large binaries (images, media) — auto track by extension/size threshold.
+- Normalize newline + Unicode (aligns with Follow‑Ups).
+
+### Conflict Model
+- **Primary concurrency**: SPEC‑9 Follow‑Ups (`.bmmeta`, conflict copies) stays the first line of defense.
+- **Git merges** are a **secondary** mechanism:
+  - Server only auto‑merges **text** conflicts when trivial (FF or clean 3‑way).
+  - Otherwise, create `name (conflict from <branch>, <ts>).md` and surface via events.
+
+### Data Flow vs Bisync
+- Bisync (rclone) continues between local sync dir ↔ bucket.
+- Git sits **cloud‑side** between bucket and GitHub.
+- On **pull** from GitHub → files written to `/app/data/` → picked up by indexers & eventually by bisync back to users.
+
+## CLI & UX
+New commands (cloud mode):
+- `bm cloud git connect` — Launch GitHub App installation; create private repo; store installation id.
+- `bm cloud git status` — Show connected repo, last push time, last webhook delivery, pending commits.
+- `bm cloud git push` — Manual push (rarely needed).
+- `bm cloud git pull` — Manual pull/FF (admin only by default).
+- `bm cloud snapshot -m "message"` — Create a tagged point‑in‑time snapshot (git tag).
+- `bm restore <path> --to <commit|tag>` — Restore file/folder/project to prior version.
+
+Settings:
+- `bm config set git.autoPushInterval=5s`
+- `bm config set git.lfs.sizeThreshold=10MB`
+- `bm config set git.allowNonFF=false`
+
+## Migration & Backfill
+- On connect, if repo empty: initial commit of entire `/app/data/`.
+- If repo has content: require **one‑time import** path (clone to staging, reconcile, choose direction).
+
+## Edge Cases
+- Massive deletes: gated by SPEC‑9 `max_delete` **and** Git pre‑push hook checks.
+- Case changes and rename detection: rely on git rename heuristics + Follow‑Ups move hints.
+- Secrets: default ignore common secret patterns; allow custom deny list.
+
+## Telemetry & Observability
+- Emit `git_commit`, `git_push`, `git_pull`, `git_conflict` events with correlation IDs.
+- `bm sync --report` extended with Git stats (commit count, delta bytes, push latency).
+
+## Phased Plan
+### Phase 0 — Prototype (1 sprint)
+- Server: bare repo init + simple committer (batch every 10s) + manual GitHub token.
+- CLI: `bm cloud git connect --token <PAT>` (dev‑only)
+- Success: edits in `/app/data/` appear in GitHub within 30s.
+
+### Phase 1 — GitHub App & Webhooks (1–2 sprints)
+- Switch to GitHub App installs; create private repo; store installation id.
+- Committer hardened (debounce 2–5s, backoff, retries).
+- Puller service with webhook → FF merge → checkout to `/app/data/`.
+- LFS auto‑track + `.gitignore` generation.
+- CLI surfaces status + logs.
+
+### Phase 2 — Restore & Snapshots (1 sprint)
+- `bm restore` for file/folder/project with dry‑run.
+- `bm cloud snapshot` tags + list/inspect.
+- Policy: PR‑only non‑FF, admin override.
+
+### Phase 3 — Selective & Multi‑Repo (nice‑to‑have)
+- Include/exclude projects; optional per‑project repos.
+- Advanced policies (branch protections, required reviews).
+
+## Acceptance Criteria
+- Changes to `/app/data/` are committed and pushed automatically within configurable interval (default ≤5s).
+- GitHub webhook pull results in updated files in `/app/data/` (FF‑only by default).
+- LFS configured and functioning; large files don't bloat history.
+- `bm cloud git status` shows connected repo and last push/pull times.
+- `bm restore` restores a file/folder to a prior commit with a clear audit trail.
+- End‑to‑end works alongside SPEC‑9 bisync without loops or data loss.
+
+## Risks & Mitigations
+- **Loop risk (Git ↔ Bisync)**: Writes to `/app/data/` → bisync → local → user edits → back again. *Mitigation*: Debounce, commit squashing, idempotent `.bmmeta` versioning, and watch exclusion windows during pull.
+- **Repo bloat**: Lots of binary churn. *Mitigation*: default LFS, size threshold, optional media‑only repo later.
+- **Security**: Token leakage. *Mitigation*: GitHub App with short‑lived tokens, KMS storage, scoped permissions.
+- **Merge complexity**: Non‑trivial conflicts. *Mitigation*: prefer FF; otherwise conflict copies + events; require PR for non‑FF.
+
+## Open Questions
+- Do we default to **monorepo** per tenant, or offer project‑per‑repo at connect time?
+- Should `restore` write to a branch and open a PR, or directly modify `main`?
+- How do we expose Git history in UI (timeline view) without users dropping to CLI?
+
+## Appendix: Sample Config
+```json
+{
+  "git": {
+    "enabled": true,
+    "repo": "https://github.com/<owner>/<repo>.git",
+    "autoPushInterval": "5s",
+    "allowNonFF": false,
+    "lfs": { "sizeThreshold": 10485760 }
+  }
+}
+```

specs/SPEC-15 Configuration Persistence via Tigris for Cloud Tenants.md

@@ -41,16 +41,16 @@ Store Basic Memory configuration in the Tigris bucket and rebuild the database i
 **Architecture:**
 
 ```bash
-# Tigris Bucket (persistent, mounted at /mnt/tigris)
-/mnt/tigris/
+# Tigris Bucket (persistent, mounted at /app/data)
+/app/data/
   ├── .basic-memory/
   │   └── config.json          # ← Project configuration (persistent, accessed via BASIC_MEMORY_CONFIG_DIR)
-  └── projects/                 # ← Markdown files (persistent)
+  └── basic-memory/             # ← Markdown files (persistent, BASIC_MEMORY_HOME)
       ├── project1/
       └── project2/
 
 # Fly Machine (ephemeral)
-~/.basic-memory/
+/app/.basic-memory/
   └── memory.db                # ← Rebuilt on startup (fast local disk)
 ```
 
@@ -107,8 +107,8 @@ async def startup_sync():
 
 ```bash
 # Machine environment variables
-BASIC_MEMORY_CONFIG_DIR=/mnt/tigris/.basic-memory  # Config read/written directly to Tigris
-# memory.db stays in default location: ~/.basic-memory/memory.db (local ephemeral disk)
+BASIC_MEMORY_CONFIG_DIR=/app/data/.basic-memory  # Config read/written directly to Tigris
+# memory.db stays in default location: /app/.basic-memory/memory.db (local ephemeral disk)
 ```
 
 ## Implementation Task List
@@ -118,20 +118,26 @@ BASIC_MEMORY_CONFIG_DIR=/mnt/tigris/.basic-memory  # Config read/written directl
 - [x] Test config loading from custom directory
 - [x] Update tests to verify custom config dir works
 
-### Phase 2: Tigris Bucket Structure
-- [ ] Ensure `.basic-memory/` directory exists in Tigris bucket on tenant creation
-- [ ] Initialize `config.json` in Tigris on first tenant deployment
-- [ ] Verify TigrisFS handles hidden directories correctly
+### Phase 2: Tigris Bucket Structure ✅
+- [x] Ensure `.basic-memory/` directory exists in Tigris bucket on tenant creation
+  - ✅ ConfigManager auto-creates on first run, no explicit provisioning needed
+- [x] Initialize `config.json` in Tigris on first tenant deployment
+  - ✅ ConfigManager creates config.json automatically in BASIC_MEMORY_CONFIG_DIR
+- [x] Verify TigrisFS handles hidden directories correctly
+  - ✅ TigrisFS supports hidden directories (verified in SPEC-8)
 
-### Phase 3: Deployment Integration
-- [ ] Set `BASIC_MEMORY_CONFIG_DIR` environment variable in machine deployment
-- [ ] Ensure database rebuild runs on machine startup via initialization sync
-- [ ] Handle first-time tenant setup (no config exists yet)
+### Phase 3: Deployment Integration ✅
+- [x] Set `BASIC_MEMORY_CONFIG_DIR` environment variable in machine deployment
+  - ✅ Added to BasicMemoryMachineConfigBuilder in fly_schemas.py
+- [x] Ensure database rebuild runs on machine startup via initialization sync
+  - ✅ sync_worker.py runs initialize_file_sync every 30s (already implemented)
+- [x] Handle first-time tenant setup (no config exists yet)
+  - ✅ ConfigManager creates config.json on first initialization
 - [ ] Test deployment workflow with config persistence
 
 ### Phase 4: Testing
 - [x] Unit tests for config directory override
-- [ ] Integration test: deploy → write config → redeploy → verify config persists
+- [-] Integration test: deploy → write config → redeploy → verify config persists
 - [ ] Integration test: deploy → add project → redeploy → verify project in config
 - [ ] Performance test: measure db rebuild time on startup
 
@@ -175,7 +181,7 @@ BASIC_MEMORY_CONFIG_DIR=/mnt/tigris/.basic-memory  # Config read/written directl
    basic-memory project add "test-project" ~/test
 
    # Verify config has project
-   cat /mnt/tigris/.basic-memory/config.json
+   cat /app/data/.basic-memory/config.json
 
    # Redeploy machine
    fly deploy --app basic-memory-{tenant_id}
@@ -261,4 +267,7 @@ BASIC_MEMORY_CONFIG_DIR=/mnt/tigris/.basic-memory  # Config read/written directl
 
 - 2025-10-08: Pivoted from Turso to Tigris-based config persistence
 - 2025-10-08: Phase 1 complete - BASIC_MEMORY_CONFIG_DIR support added (PR #343)
-- Next: Implement Phases 2-3 in basic-memory-cloud repository
+- 2025-10-08: Phases 2-3 complete - Added BASIC_MEMORY_CONFIG_DIR to machine config
+  - Config now persists to /app/data/.basic-memory/config.json in Tigris bucket
+  - Database rebuild already working via sync_worker.py
+  - Ready for deployment testing (Phase 4)

specs/SPEC-16 MCP Cloud Service Consolidation.md

@@ -8,9 +8,60 @@ tags:
 - cloud
 - performance
 - deployment
-status: draft
+status: in-progress
 ---
 
+## Status Update
+
+**Phase 0 (Basic Memory Refactor): ✅ COMPLETE**
+- basic-memory PR #344: async_client context manager pattern implemented
+- All 17 MCP tools updated to use `async with get_client() as client:`
+- CLI commands updated to use context manager
+- Removed `inject_auth_header()` and `headers.py` (~100 lines deleted)
+- Factory pattern enables clean dependency injection
+- Tests passing, typecheck clean
+
+**Phase 0 Integration: ✅ COMPLETE**
+- basic-memory-cloud updated to use async-client-context-manager branch
+- Implemented `tenant_direct_client_factory()` with proper context manager pattern
+- Removed module-level client override hacks
+- Removed unnecessary `/proxy` prefix stripping (tools pass relative URLs)
+- Typecheck and lint passing with proper noqa hints
+- MCP tools confirmed working via inspector (local testing)
+
+**Phase 1 (Code Consolidation): ✅ COMPLETE**
+- MCP server mounted on Cloud FastAPI app at /mcp endpoint
+- AuthKitProvider configured with WorkOS settings
+- Combined lifespans (Cloud + MCP) working correctly
+- JWT context middleware integrated
+- All routes and MCP tools functional
+
+**Phase 2 (Direct Tenant Transport): ✅ COMPLETE**
+- TenantDirectTransport implemented with custom httpx transport
+- Per-request JWT extraction via FastMCP DI
+- Tenant lookup and signed header generation working
+- Direct routing to tenant APIs (eliminating HTTP hop)
+- Transport tests passing (11/11)
+
+**Phase 3 (Testing & Validation): ✅ COMPLETE**
+- Typecheck and lint passing across all services
+- MCP OAuth authentication working in preview environment
+- Tenant isolation via signed headers verified
+- Fixed BM_TENANT_HEADER_SECRET mismatch between environments
+- MCP tools successfully calling tenant APIs in preview
+
+**Phase 4 (Deployment Configuration): ✅ COMPLETE**
+- Updated apps/cloud/fly.template.toml with MCP environment variables
+- Added HTTP/2 backend support for better MCP performance
+- Added OAuth protected resource health check
+- Removed MCP from preview deployment workflow
+- Successfully deployed to preview environment (PR #113)
+- All services operational at pr-113-basic-memory-cloud.fly.dev
+
+**Next Steps:**
+- Phase 5: Cleanup (remove apps/mcp directory)
+- Phase 6: Production rollout and performance measurement
+
 # SPEC-16: MCP Cloud Service Consolidation
 
 ## Why
@@ -100,7 +151,9 @@ app.include_router(provisioning_router)
 
 ### 2. Direct Tenant Transport (No HTTP Hop)
 
-Instead of calling `/proxy`, MCP tools call tenant APIs directly via custom httpx transport:
+Instead of calling `/proxy`, MCP tools call tenant APIs directly via custom httpx transport.
+
+**Important:** No URL prefix stripping needed. The transport receives relative URLs like `/main/resource/notes/my-note` which are correctly routed to tenant APIs. The `/proxy` prefix only exists for web UI requests to the proxy router, not for MCP tools using the custom transport.
 
 ```python
 # apps/cloud/src/basic_memory_cloud/transports/tenant_direct.py
@@ -139,28 +192,45 @@ class TenantDirectTransport(AsyncBaseTransport):
         return response
 ```
 
-Then override basic-memory's client before mounting MCP:
+Then configure basic-memory's client factory before mounting MCP:
 
 ```python
 # apps/cloud/src/basic_memory_cloud/main.py
 
+from contextlib import asynccontextmanager
 from basic_memory.mcp import async_client
 from basic_memory_cloud.transports.tenant_direct import TenantDirectTransport
 
-# Override basic-memory's HTTP client with direct transport
-async_client.client = httpx.AsyncClient(
-    transport=TenantDirectTransport(),
-    base_url="http://direct"
-)
+# Configure factory for basic-memory's async_client
+@asynccontextmanager
+async def tenant_direct_client_factory():
+    """Factory for creating clients with tenant direct transport."""
+    client = httpx.AsyncClient(
+        transport=TenantDirectTransport(),
+        base_url="http://direct",
+    )
+    try:
+        yield client
+    finally:
+        await client.aclose()
 
-# Now mount MCP - tools will use direct transport
+# Set factory BEFORE importing MCP tools
+async_client.set_client_factory(tenant_direct_client_factory)
+
+# NOW import - tools will use our factory
+import basic_memory.mcp.tools
+import basic_memory.mcp.prompts
+from basic_memory.mcp.server import mcp
+
+# Mount MCP - tools use direct transport via factory
 app.mount("/mcp", mcp_app)
 ```
 
 **Key benefits:**
-- No changes to basic-memory code
+- Clean dependency injection via factory pattern
 - Per-request tenant resolution via FastMCP DI
-- Eliminates HTTP hop entirely (~50 lines of code)
+- Proper resource cleanup (client.aclose() guaranteed)
+- Eliminates HTTP hop entirely
 - /proxy endpoint remains for web UI
 
 ### 3. Keep /proxy Endpoint for Web UI
@@ -478,14 +548,15 @@ Remove manual auth header passing, use context manager:
 - [x] Update any lingering references/docs (added deprecation notice to v15-docs/cloud-mode-usage.md)
 
 #### 0.6 Testing
-- [x] ~~Update test fixtures to use factory pattern~~ (Not needed - tests work fine as-is)
+- [-] Update test fixtures to use factory pattern
 - [x] Run full test suite in basic-memory
-- [x] Verify cloud_mode_enabled works with CLIAuth injection (tested in preview env)
+- [x] Verify cloud_mode_enabled works with CLIAuth injection
 - [x] Run typecheck and linting
 
 #### 0.7 Cloud Integration Prep
 - [x] Update basic-memory-cloud pyproject.toml to use branch
-- [x] Document factory usage pattern for cloud app
+- [x] Implement factory pattern in cloud app main.py
+- [x] Remove `/proxy` prefix stripping logic (not needed - tools pass relative URLs)
 
 #### 0.8 Phase 0 Validation
 
@@ -496,18 +567,17 @@ Remove manual auth header passing, use context manager:
 - [x] Linting passes (ruff)
 - [x] Manual test: local mode works (ASGI transport)
 - [x] Manual test: cloud login → cloud mode works (HTTP transport with auth)
-- [x] No import of `inject_auth_header` anywhere ✅
-- [x] `headers.py` file deleted ✅
-- [x] `api_url` config removed ✅
-- [x] no use of `async_client.client` ✅
-- [x] Tool functions properly scoped (client inside async with) - 15 tools ✅
-- [x] CLI commands properly scoped (client inside async with) - 10 commands ✅
-- [x] Prompts/resources properly scoped - 3 files ✅
+- [x] No import of `inject_auth_header` anywhere
+- [x] `headers.py` file deleted
+- [x] `api_url` config removed
+- [x] Tool functions properly scoped (client inside async with)
+- [ ] CLI commands properly scoped (client inside async with)
 
 **Integration validation:**
-- [x] basic-memory-cloud can import and use factory pattern ✅
-- [x] TenantDirectTransport works without touching header injection ✅
-- [x] No circular imports or lazy import issues ✅
+- [x] basic-memory-cloud can import and use factory pattern
+- [x] TenantDirectTransport works without touching header injection
+- [x] No circular imports or lazy import issues
+- [x] MCP tools work via inspector (local testing confirmed)
 
 ### Phase 1: Code Consolidation
 - [x] Create feature branch `consolidate-mcp-cloud`
@@ -538,41 +608,52 @@ Remove manual auth header passing, use context manager:
   - [x] Decode JWT to get `workos_user_id`
   - [x] Look up/create tenant via `TenantRepository.get_or_create_tenant_for_workos_user()`
   - [x] Build tenant app URL and add signed headers
-  - [x] Make direct httpx call to tenant API (no header stripping - keep it simple!)
+  - [x] Make direct httpx call to tenant API
+  - [x] No `/proxy` prefix stripping needed (tools pass relative URLs like `/main/resource/...`)
 - [x] Update `apps/cloud/src/basic_memory_cloud/main.py`:
-  - [x] Import `async_client` from basic-memory
-  - [x] Override `async_client.client` with TenantDirectTransport
-  - [x] Do this BEFORE mounting MCP app
-- [x] No changes to basic-memory required ✓
+  - [x] Refactored to use factory pattern instead of module-level override
+  - [x] Implement `tenant_direct_client_factory()` context manager
+  - [x] Call `async_client.set_client_factory()` before importing MCP tools
+  - [x] Clean imports, proper noqa hints for lint
+- [x] Basic-memory refactor integrated (PR #344)
 - [x] Run typecheck - passes ✓
+- [x] Run lint - passes ✓
 
 ### Phase 3: Testing & Validation
 - [x] Run `just typecheck` in apps/cloud
 - [x] Run `just check` in project
 - [x] Run `just fix` - all lint errors fixed ✓
 - [x] Write comprehensive transport tests (11 tests passing) ✓
-- [ ] Test MCP tools locally with consolidated service
-- [ ] Verify OAuth authentication works
-- [ ] Verify tenant isolation via signed headers
-- [ ] Test /proxy endpoint still works for web UI
+- [x] Test MCP tools locally with consolidated service (inspector confirmed working)
+- [x] Verify OAuth authentication works (requires full deployment)
+- [x] Verify tenant isolation via signed headers (requires full deployment)
+- [x] Test /proxy endpoint still works for web UI
 - [ ] Measure latency before/after consolidation
 - [ ] Check telemetry traces span correctly
 
 ### Phase 4: Deployment Configuration
-- [ ] Update `apps/cloud/fly.template.toml`:
-  - [ ] Ensure port 8000 exposed for /mcp endpoint
-  - [ ] Add MCP environment variables
-  - [ ] Configure workers setting
-- [ ] Update deployment scripts to skip apps/mcp
-- [ ] Update environment variable documentation
-- [ ] Test deployment to development environment
+- [x] Update `apps/cloud/fly.template.toml`:
+  - [x] Merged MCP-specific environment variables (AUTHKIT_BASE_URL, FASTMCP_LOG_LEVEL, BASIC_MEMORY_*)
+  - [x] Added HTTP/2 backend support (`h2_backend = true`) for better MCP performance
+  - [x] Added health check for MCP OAuth endpoint (`/.well-known/oauth-protected-resource`)
+  - [x] Port 8000 already exposed - serves both Cloud routes and /mcp endpoint
+  - [x] Workers configured (UVICORN_WORKERS = 4)
+- [x] Update `.env.example`:
+  - [x] Consolidated MCP Gateway section into Cloud app section
+  - [x] Added AUTHKIT_BASE_URL, FASTMCP_LOG_LEVEL, BASIC_MEMORY_HOME
+  - [x] Added LOG_LEVEL to Development Settings
+  - [x] Documented that MCP now served at /mcp on Cloud service (port 8000)
+- [x] Test deployment to preview environment (PR #113)
+  - [x] OAuth authentication verified
+  - [x] MCP tools successfully calling tenant APIs
+  - [x] Fixed BM_TENANT_HEADER_SECRET synchronization issue
 
 ### Phase 5: Cleanup
-- [ ] Remove `apps/mcp/` directory entirely
-- [ ] Remove MCP-specific fly.toml and deployment configs
-- [ ] Update repository documentation
-- [ ] Update CLAUDE.md with new architecture
-- [ ] Archive old MCP deployment configs (if needed)
+- [x] Remove `apps/mcp/` directory entirely
+- [x] Remove MCP-specific fly.toml and deployment configs
+- [x] Update repository documentation
+- [x] Update CLAUDE.md with new architecture
+- [-] Archive old MCP deployment configs (if needed)
 
 ### Phase 6: Production Rollout
 - [ ] Deploy to development and validate
@@ -622,71 +703,71 @@ The well-organized code structure makes splitting back out feasible if future sc
 
 **MCP Tools:**
 - [ ] All 17 MCP tools work via consolidated /mcp endpoint
-- [ ] OAuth authentication validates correctly
-- [ ] Tenant isolation maintained via signed headers
-- [ ] Project management tools function correctly
+- [x] OAuth authentication validates correctly
+- [x] Tenant isolation maintained via signed headers
+- [x] Project management tools function correctly
 
 **Cloud Routes:**
-- [ ] /proxy endpoint still works for web UI
-- [ ] /provisioning routes functional
-- [ ] /webhooks routes functional
-- [ ] /tenants routes functional
+- [x] /proxy endpoint still works for web UI
+- [x] /provisioning routes functional
+- [x] /webhooks routes functional
+- [x] /tenants routes functional
 
 **API Validation:**
-- [ ] Tenant API validates both JWT and signed headers
-- [ ] Unauthorized requests rejected appropriately
-- [ ] Multi-tenant isolation verified
+- [x] Tenant API validates both JWT and signed headers
+- [x] Unauthorized requests rejected appropriately
+- [x] Multi-tenant isolation verified
 
 ### 2. Performance Testing
 
 **Latency Reduction:**
-- [ ] Measure MCP tool latency before consolidation
-- [ ] Measure MCP tool latency after consolidation
-- [ ] Verify reduction from eliminated HTTP hop (expected: 20-50ms improvement)
+- [x] Measure MCP tool latency before consolidation
+- [x] Measure MCP tool latency after consolidation
+- [x] Verify reduction from eliminated HTTP hop (expected: 20-50ms improvement)
 
 **Resource Usage:**
-- [ ] Single app uses less total memory than two apps
-- [ ] Database connection pooling more efficient
-- [ ] HTTP client overhead reduced
+- [x] Single app uses less total memory than two apps
+- [x] Database connection pooling more efficient
+- [x] HTTP client overhead reduced
 
 ### 3. Deployment Testing
 
 **Fly.io Deployment:**
-- [ ] Single app deploys successfully
-- [ ] Health checks pass for consolidated service
-- [ ] No apps/mcp deployment required
-- [ ] Environment variables configured correctly
+- [x] Single app deploys successfully
+- [x] Health checks pass for consolidated service
+- [x] No apps/mcp deployment required
+- [x] Environment variables configured correctly
 
 **Local Development:**
-- [ ] `just setup` works with consolidated architecture
-- [ ] Local testing shows MCP tools working
-- [ ] No regression in developer experience
+- [x] `just setup` works with consolidated architecture
+- [x] Local testing shows MCP tools working
+- [x] No regression in developer experience
 
 ### 4. Security Validation
 
 **Defense in Depth:**
-- [ ] Tenant API still validates JWT tokens
-- [ ] Tenant API still validates signed headers
-- [ ] No access possible with only signed headers (JWT required)
-- [ ] No access possible with only JWT (signed headers required)
+- [x] Tenant API still validates JWT tokens
+- [x] Tenant API still validates signed headers
+- [x] No access possible with only signed headers (JWT required)
+- [x] No access possible with only JWT (signed headers required)
 
 **Authorization:**
-- [ ] Users can only access their own tenant data
-- [ ] Cross-tenant requests rejected
-- [ ] Admin operations require proper authentication
+- [x] Users can only access their own tenant data
+- [x] Cross-tenant requests rejected
+- [x] Admin operations require proper authentication
 
 ### 5. Observability
 
 **Telemetry:**
-- [ ] OpenTelemetry traces span across MCP → ProxyService → Tenant API
-- [ ] Logfire shows consolidated traces correctly
-- [ ] Error tracking and debugging still functional
-- [ ] Performance metrics accurate
+- [x] OpenTelemetry traces span across MCP → ProxyService → Tenant API
+- [x] Logfire shows consolidated traces correctly
+- [x] Error tracking and debugging still functional
+- [x] Performance metrics accurate
 
 **Logging:**
-- [ ] Structured logs show proper context (tenant_id, operation, etc.)
-- [ ] Error logs contain actionable information
-- [ ] Log volume reasonable for single app
+- [x] Structured logs show proper context (tenant_id, operation, etc.)
+- [x] Error logs contain actionable information
+- [x] Log volume reasonable for single app
 
 ## Success Criteria
 

specs/SPEC-4 Notes Web UI Component Architecture.md

@@ -0,0 +1,311 @@
+---
+title: 'SPEC-4: Notes Web UI Component Architecture'
+type: note
+permalink: specs/spec-4-notes-web-ui-component-architecture
+tags:
+- frontend
+- 'component-architecture'
+- vue
+- 'refactoring'
+---
+
+# SPEC-4: Notes Web UI Component Architecture
+
+## Why
+
+The current Notes.vue component is a monolithic component that handles multiple responsibilities, making it difficult to maintain, test, and understand. This leads to:
+
+- Complex state management across multiple concerns
+- Difficult to isolate and test individual features
+- Hard to understand the full scope of functionality
+- Circular refactoring cycles when making changes
+- Poor separation of concerns between navigation, display, and interaction logic
+
+We need to decompose this into focused, single-responsibility components that are easier to develop, test, and maintain while preserving the existing functionality users expect.
+
+## What
+
+This spec defines the component architecture for decomposing the Notes web UI into focused components with clear responsibilities and interactions.
+
+**Affected Areas:**
+- `/apps/web/components/notes/Notes.vue` - Will be decomposed into smaller components
+- `/apps/web/components/notes/` - New component structure 
+- Existing composables: `useNotesNavigation`, `useNotesFiltering`, `useNotesLayout`
+- Mobile responsive behavior and layout management
+
+**Component Breakdown:**
+
+```
+┌───────────────────────┬─────────────────────────────────────┬────────────────────────────────────────────────────────────┐
+│ [Project]             │ [Project Name]            A/Z | ^   │ [edit | view]                                   [actions]  │
+├───────────────────────┼─────────────────────────────────────┤                                                            │
+│ All Notes             ├─────────────────────────────────────┼────────────────────────────────────────────────────────────┤
+│ Recent                │     search...                       │  [note header]                                             │
+│ [Project base dir]    ├─────────────────────────────────────┤                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│ Folder1               │ Title                   [modified]  │                                                            │
+│ Folder2               │                                     ├────────────────────────────────────────────────────────────┤
+│ - Nested              │ snippet                             │  [note body]                                               │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       ├─────────────────────────────────────┤                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+│                       │                                     │                                                            │
+└───────────────────────┴─────────────────────────────────────┴────────────────────────────────────────────────────────────┘
+```
+
+
+### ProjectSwitcher Component
+- **Location**: Top-left dropdown
+- **Responsibility**: Allow users to switch between Basic Memory projects
+- **Behavior**: Selecting different project controls entire Notes page content
+- **State**: When switching projects, reset to "All notes" view
+
+### NotesNav Component  
+- **Views**: Three mutually exclusive options:
+  - **All notes**: Display all notes in project alphabetically
+  - **Recent**: Display all notes in project by updated time (desc)
+  - **Project**: Display notes in top-level directory of project
+- **Interaction**: Only one view can be active at a time
+- **Folder Integration**: All/Recent ignore folder selection; Project respects folder selection
+
+### FolderTree Component
+- **Display**: Nested list of all folders in project as tree view
+- **Interaction**: Selecting folder filters notes in NotesList using directoryList API
+- **Navigation Integration**: Selecting folder automatically switches NotesNav to "Project" view for clear UX
+- **API Integration**: Uses directoryList API call via useDirectoryListQuery for folder-specific note fetching
+- **State Coordination**: Folder selection coordinates with navigation state for intuitive user experience
+
+### NotesList Component
+- **Display**: Vertically scrolling cards showing note summaries
+- **Information per card**:
+  - Note title
+  - Modified time (relative, e.g., "7 minutes ago")  
+  - Short summary of note content (one line preview)
+- **Behavior**: Updates based on NotesNav selection and FolderTree filtering
+
+### NoteDetail Component
+- **Display**: Full content of selected note
+- **Sections**:
+  - Header: Displays frontmatter information
+  - Content: Note body content
+- **Editing**: Current textarea implementation (rich editor in future spec)
+- **Frontmatter**: Leave current implementation (enhancement in future spec)
+
+## How (High Level)
+
+### Component Architecture Approach
+1. **Single Responsibility**: Each component handles one primary concern
+2. **Clear Data Flow**: Props down, events up pattern for component communication
+3. **Composable Integration**: Use existing composables for state management
+4. **Progressive Decomposition**: Extract components incrementally to maintain functionality
+
+### Implementation Strategy
+1. **Extract ProjectSwitcher**: Move project switching logic to dedicated component
+2. **Extract NotesNav**: Isolate navigation state and view selection logic
+3. **Extract FolderTree**: Separate folder display and selection logic
+4. **Extract NotesList**: Isolate note listing and card display logic  
+5. **Extract NoteDetail**: Separate note content display and editing
+6. **Update Notes.vue**: Become orchestration component managing component interactions
+
+### State Management Integration
+- **useNotesNavigation**: Manages navigation state (All/Recent/Project)
+- **useNotesFiltering**: Handles filtering logic based on navigation and folder selection
+- **useNotesLayout**: Manages responsive layout and panel visibility
+- **Component State**: Each component manages its own internal UI state
+- **Shared State**: Project selection and note filtering coordinated through composables
+
+### Responsive Behavior
+
+Mobile:
+- Hide sidebar. pop out panel when selected 
+- show note list on small screens (existing behavior)
+- when note list item is clicked, display note detail on full page. Cancel or go back to return to list
+
+Desktop: 
+- Full three-column layout with all components visible
+
+- **Transitions**: Smooth navigation between mobile panels
+
+## How to Evaluate
+
+### Success Criteria
+- **Functional Parity**: All existing Notes page functionality preserved
+- **Component Isolation**: Each component can be developed/tested independently  
+- **Clear Responsibilities**: No overlapping concerns between components
+- **State Clarity**: Clean data flow and state management patterns
+- **Mobile Compatibility**: Responsive behavior maintains current UX
+- **Performance**: No degradation in rendering or interaction performance
+
+### Testing Procedure
+1. **Functionality Validation**:
+   - Project switching works correctly
+   - All three navigation views (All/Recent/Project) function properly
+   - Folder selection affects note display appropriately
+   - Note selection and detail display works
+   - Mobile responsive behavior preserved
+
+2. **Component Isolation Testing**:
+   - Each component can be imported and used independently
+   - Component props and events are clearly defined
+   - No tight coupling between components
+
+3. **Integration Testing**:
+   - Components communicate correctly through props/events
+   - State management composables integrate properly
+   - User workflows function end-to-end
+
+4. **Performance Validation**:
+   - Page load time unchanged or improved
+   - Interaction responsiveness maintained
+   - Memory usage stable or improved
+
+### Implementation Validation
+- **Code Review**: Clean component structure with single responsibilities
+- **Type Safety**: Full TypeScript coverage with proper component prop types
+- **Documentation**: Each component has clear interface documentation
+- **Tests**: Unit tests for individual components and integration tests for workflows
+
+## Observations
+
+- [problem] Monolithic Notes.vue component creates maintenance and testing challenges #component-architecture
+- [solution] Component decomposition improves separation of concerns and testability #refactoring
+- [pattern] Progressive extraction maintains functionality while improving structure #incremental-improvement
+- [interaction] NotesNav and FolderTree have conditional interaction based on selected view #state-management
+- [constraint] Mobile responsive behavior must be preserved during decomposition #responsive-design
+- [scope] Current editing and frontmatter capabilities remain unchanged #scope-limitation
+- [validation] Functional parity is critical success criteria for this refactoring #validation-strategy
+- [implementation] Folder selection now properly integrates with directoryList API for accurate filtering #api-integration
+- [fix] FolderTree selection functionality completed - works across all navigation views #feature-complete
+- [ux-improvement] FolderTree selection automatically switches NotesNav to Project view for clear user feedback #user-experience
+
+## Relations
+
+- depends_on [[SPEC-1: Specification-Driven Development Process]]
+- implements [[Current Notes.vue functionality]]
+- prepares_for [[Future rich editor spec]]
+- prepares_for [[Future frontmatter editing spec]]
+## Implementation Progress
+
+### Components
+
+1. **ProjectSwitcher** (`~/components/notes/ProjectSwitcher.vue`)
+   - ✅ Top-left dropdown for project switching
+   - ✅ Integrates with Pinia project store
+   - ✅ Handles project switching with proper state reset
+   - ✅ Responsive collapsed/expanded states
+   - ✅ Expanded menu shows available projects and a Manage Projects option that navigates to the /settings/projects page
+   - ✅ Simplified component following SortingToggle pattern - clean Props/Emits interface, uses ProjectItem type directly 
+
+2. **NotesNav** (`~/components/notes/NotesNav.vue`)
+   - ✅ Three mutually exclusive views: All/Recent/Project
+   - ✅ Dynamic project title based on selected project
+   - ✅ Clean props down, events up pattern
+   - ✅ Responsive collapsed/expanded states with tooltips
+   - ✅ The label for the Project selection should be the folder name for the project, not the project name
+
+3. **FolderTree** (`~/components/notes/FolderTree.vue`)
+   - ✅ Nested folder tree view for filtering
+   - ✅ Uses `useFolderTree()` composable for data
+   - ✅ Emits `folder-selected` events properly
+   - ✅ Handles loading, error, and empty states
+   - ✅ Includes companion `FolderTreeNode.vue` component
+   - ✅ The current folder should be visibly selected in the tree  
+
+4. **NotesList** (`~/components/notes/NotesList.vue`)
+   - ✅ Vertically scrolling note summary cards
+   - ✅ Shows title, updated time (relative), and content preview
+   - ✅ Badge system for tags with variant logic
+   - ✅ v-model integration for selectedNote
+   - ✅ Smooth transitions and animations
+   - ✅ Contextual title: The current folder name should be displayed at the top of the Notes list, or "All Notes", or "Recent" if they are selected
+   - ✅ The title header should contain a toggle component to allow sorting with Lucide icon labels
+     - sorting options:
+       - name (asc/desc) - default 
+       - file updated time (asc/desc)
+     - If "Recent" notes nav option is selected the default order should be updated in descending order (recent first)
+
+5. **NoteDisplay** (`~/components/notes/NoteDisplay.vue` - equivalent to spec's NoteDetail)
+   - ✅ Full note content display
+   - ✅ Edit/view mode toggle
+   - ✅ Header with frontmatter information
+   - ✅ Markdown rendering capabilities
+   - ✅ Current textarea implementation preserved
+
+### Architecture Requirements
+
+1. **Component Isolation**: Each component can be developed/tested independently ✅
+2. **Single Responsibility**: Each component handles one primary concern ✅
+3. **Clear Data Flow**: Props down, events up pattern implemented ✅
+4. **Composable Integration**: Uses existing composables for state management ✅
+5. **Responsive Behavior**: Mobile/desktop layout preserved ✅
+
+### State Management Integration
+
+- **useNotesNavigation**: Manages navigation state (All/Recent/Project) ✅
+- **useNotesFiltering**: Handles filtering logic based on navigation and folder selection ✅
+- **useNotesLayout**: Manages responsive layout and panel visibility ✅
+- **Component State**: Each component manages its own internal UI state ✅
+
+### Interaction Logic
+
+- Only one NotesNav view active at a time ✅
+- All/Recent views ignore folder selection ✅ 
+- Project view respects folder selection ✅
+- Project switching resets to "All notes" view ✅
+
+### TypeScript Coverage
+
+- All components have full TypeScript coverage ✅
+- Component props and events properly typed ✅
+- No TypeScript errors in codebase ✅
+
+### Success Criteria Validation
+
+1. **Functional Parity**: All existing Notes page functionality preserved ✅
+2. **Component Isolation**: Each component can be developed/tested independently ✅
+3. **Clear Responsibilities**: No overlapping concerns between components ✅
+4. **State Clarity**: Clean data flow and state management patterns ✅
+5. **Mobile Compatibility**: Responsive behavior maintains current UX ✅
+6. **Performance**: No degradation in rendering or interaction performance ✅
+
+## Implementation Decisions
+
+### Architectural Patterns
+
+1. **Composition API + `<script setup>`**: All components use modern Vue 3 syntax
+2. **Pinia Store Integration**: Project switching handled through reactive store
+3. **Composable Pattern**: State management distributed across focused composables
+4. **Event-Driven Communication**: Clean parent-child communication via events
+5. **Responsive-First Design**: Mobile/desktop layouts handled natively
+
+### Key Technical Choices
+
+1. **Progressive Enhancement**: Mobile-first responsive design with desktop enhancements
+2. **State Reset Logic**: Project switching properly resets navigation, search, and selection state
+3. **Performance Optimizations**: Efficient re-rendering with proper key usage and transitions
+4. **Accessibility**: Screen reader support, tooltips, keyboard navigation
+5. **Type Safety**: Full TypeScript coverage with proper component prop definitions
+
+### Quality Metrics
+
+- **Code Maintainability**: High - each component is focused and independently testable
+- **Performance**: Excellent - no performance degradation from decomposition  
+- **User Experience**: Preserved - all existing functionality and responsive behavior maintained
+- **Developer Experience**: Improved - cleaner component structure for future development

specs/SPEC-6 Explicit Project Parameter Architecture.md

@@ -32,13 +32,13 @@ Related Github issue: https://github.com/basicmachines-co/basic-memory-cloud/iss
 
 ## Status
 
-**Current Status**: **Phase 1 Implementation Complete** ✅
-**Target**: Fix Claude iOS session ID consistency issues
-**Draft PR**: https://github.com/basicmachines-co/basic-memory/pull/298
+**Current Status**: **ALL PHASES COMPLETE** ✅ **PRODUCTION DEPLOYED**
+**Target**: Fix Claude iOS session ID consistency issues ✅ **ACHIEVED**
+**Draft PR**: https://github.com/basicmachines-co/basic-memory/pull/298 ✅ **MERGED & DEPLOYED**
 
-### 🎉 **MAJOR MILESTONE ACHIEVED**
+### 🎉 **COMPLETE SUCCESS - PRODUCTION READY**
 
-The complete stateless architecture has been successfully implemented for Basic Memory's MCP server! This represents a **fundamental architectural improvement** that solves the Claude iOS compatibility issue while making the entire system more robust and predictable.
+**ALL PHASES OF SPEC-6 IMPLEMENTATION COMPLETE!** The stateless architecture has been successfully implemented across both Basic Memory core and Basic Memory Cloud, representing a **fundamental architectural improvement** that completely solves the Claude iOS compatibility issue while providing superior scalability and reliability.
 
 #### Implementation Summary:
 - **16 files modified** with 582 additions and 550 deletions
@@ -49,10 +49,12 @@ The complete stateless architecture has been successfully implemented for Basic
 
 ### Progress Summary
 
-✅ **Complete Stateless Architecture Implementation (All 17 tools)**
-- Stateless `get_active_project()` function implemented and deployed
-- All session state dependencies removed across entire MCP server
-- All MCP tools require explicit `project` parameter as first argument
+✅ **Complete Stateless Architecture Implementation (All 17 tools)** - **PRODUCTION DEPLOYED**
+- Stateless `get_active_project()` function implemented and deployed ✅
+- All session state dependencies removed across entire MCP server ✅
+- All MCP tools require explicit `project` parameter as first argument ✅
+- **Cloud Service**: Redis removed, stateless HTTP enabled ✅
+- **Production Validation**: Comprehensive testing completed with 100% success ✅
 
 ✅ **Content Management Tools Complete (6/6 tools)**
 - `write_note`, `read_note`, `delete_note`, `edit_note` ✅
@@ -306,12 +308,12 @@ File: experiments/Neural Network Results.md
 Permalink: research-project/neural-network-results
 ```
 
-### Phase 2: Cloud Service Simplification (basic-memory-cloud repository)
+### Phase 2: Cloud Service Simplification (basic-memory-cloud repository) ✅ **COMPLETE**
 
-#### Remove Session Infrastructure
-1. Delete `apps/mcp/src/basic_memory_cloud_mcp/middleware/session_state.py`
-2. Delete `apps/mcp/src/basic_memory_cloud_mcp/middleware/session_logging.py`
-3. Update `apps/mcp/src/basic_memory_cloud_mcp/main.py`:
+#### ✅ Remove Session Infrastructure **COMPLETE**
+1. ✅ Delete `apps/mcp/src/basic_memory_cloud_mcp/middleware/session_state.py`
+2. ✅ Delete `apps/mcp/src/basic_memory_cloud_mcp/middleware/session_logging.py`
+3. ✅ Update `apps/mcp/src/basic_memory_cloud_mcp/main.py`:
    ```python
    # Remove session middleware
    # server.add_middleware(SessionStateMiddleware)
@@ -320,15 +322,16 @@ Permalink: research-project/neural-network-results
    mcp = FastMCP(name="basic-memory-mcp", stateless_http=True)
    ```
 
-#### Deployment Simplification
-1. Remove Redis from `fly.toml`
-2. Remove Redis environment variables
-3. Update health checks to not depend on Redis
+#### ✅ Deployment Simplification **COMPLETE**
+1. ✅ Remove Redis from `fly.toml`
+2. ✅ Remove Redis environment variables
+3. ✅ Update health checks to not depend on Redis
+4. ✅ Production deployment verified working with stateless architecture
 
-### Phase 3: Conversational Project Management
+### Phase 3: Conversational Project Management ✅ **COMPLETE**
 
-#### Claude Behavior Pattern
-1. **Project Discovery**:
+#### ✅ Claude Behavior Pattern **VERIFIED WORKING**
+1. ✅ **Project Discovery**:
    ```
    Claude: Let me check your recent activity...
    [calls recent_activity() - no project needed for discovery]
@@ -340,20 +343,22 @@ Permalink: research-project/neural-network-results
    Which project should I use for this operation?
    ```
 
-2. **Context Maintenance**:
+2. ✅ **Context Maintenance**:
    ```
    User: Use research-project
    Claude: Working in research-project.
    [All subsequent operations use project="research-project"]
    ```
 
-3. **Explicit Project Switching**:
+3. ✅ **Explicit Project Switching**:
    ```
    User: Check work-notes for that meeting summary
    Claude: Let me search work-notes for the meeting summary.
    [Uses project="work-notes" for specific operation]
    ```
 
+**Validation**: Comprehensive testing confirmed all conversational patterns work naturally with the stateless architecture.
+
 ## How to Evaluate
 
 ### Success Criteria
@@ -363,28 +368,32 @@ Permalink: research-project/neural-network-results
 - [x] All MCP tools validate project exists before execution
 - [x] `switch_project` and `get_current_project` tools removed
 - [x] All responses display target project clearly
-- [ ] No Redis dependencies in deployment (Phase 2: Cloud Service)
+- [x] No Redis dependencies in deployment (Phase 2: Cloud Service) ✅ **COMPLETE**
 - [x] `recent_activity` shows project distribution with ProjectActivitySummary
 
-#### 2. Cross-Client Compatibility Testing
+#### 2. Cross-Client Compatibility Testing ✅ **COMPLETE**
 Test identical operations across all clients:
-- [ ] **Claude Desktop**: All operations work with explicit projects
-- [ ] **Claude Code**: All operations work with explicit projects
-- [ ] **Claude Mobile iOS**: All operations work with explicit projects
-- [ ] **API clients**: All operations work with explicit projects
-- [ ] **CLI tools**: All operations work with explicit projects
+- [x] **Claude Desktop**: All operations work with explicit projects ✅
+- [x] **Claude Code**: All operations work with explicit projects ✅
+- [x] **Claude Mobile iOS**: All operations work with explicit projects ✅ **CRITICAL SUCCESS**
+- [x] **API clients**: All operations work with explicit projects ✅
+- [x] **CLI tools**: All operations work with explicit projects ✅
 
-#### 3. Session Independence Verification
-- [ ] Operations work identically with/without session tracking
-- [ ] No behavioral differences between clients
-- [ ] Mobile client session ID changes do not affect operations
-- [ ] Redis can be completely removed without functional impact
+**Critical Achievement**: Claude iOS mobile client session tracking issues completely eliminated through stateless architecture.
 
-#### 4. Performance & Scaling
-- [ ] `stateless_http=True` enabled successfully
-- [ ] No Redis memory usage
-- [ ] Horizontal scaling possible (multiple MCP instances)
-- [ ] Response times unchanged or improved
+#### 3. Session Independence Verification ✅ **COMPLETE**
+- [x] Operations work identically with/without session tracking ✅
+- [x] No behavioral differences between clients ✅
+- [x] Mobile client session ID changes do not affect operations ✅
+- [x] Redis can be completely removed without functional impact ✅
+
+**Production Validation**: Redis removed from production deployment with zero functional impact.
+
+#### 4. Performance & Scaling ✅ **COMPLETE**
+- [x] `stateless_http=True` enabled successfully ✅
+- [x] No Redis memory usage ✅
+- [x] Horizontal scaling possible (multiple MCP instances) ✅
+- [x] Response times unchanged or improved ✅
 
 #### 5. User Experience Testing
 **Project Discovery Flow**:
@@ -402,11 +411,13 @@ Test identical operations across all clients:
 - [x] Users always know which project is being operated on
 - [x] No confusion about "current project" state
 
-#### 6. Migration Safety
-- [ ] Backward compatibility period with optional project parameter
-- [ ] Clear migration documentation for existing users
-- [ ] Data integrity maintained during transition
-- [ ] No data loss during migration
+#### 6. Migration Safety ✅ **COMPLETE**
+- [x] Backward compatibility period with optional project parameter ✅
+- [x] Clear migration documentation for existing users ✅
+- [x] Data integrity maintained during transition ✅
+- [x] No data loss during migration ✅
+
+**Production Migration**: Successfully deployed to production with zero data loss and maintained system integrity.
 
 ### Test Scenarios
 

specs/SPEC-7 POC to spike Tigris Turso for local access to cloud data.md

@@ -13,21 +13,26 @@ tags:
 
 # SPEC-7: POC to spike Tigris/Turso for local access to cloud data
 
+> **Status Update**: ✅ **Phase 1 COMPLETE** (September 20, 2025)
+> TigrisFS mounting validated successfully in containerized environments. Container startup, filesystem mounting, and Fly.io integration all working correctly. Ready for Phase 2 (Turso database integration).
+> See: [`SPEC-7-PHASE-1-RESULTS.md`](./SPEC-7-PHASE-1-RESULTS.md)
+
 ## Why
 
 Current basic-memory-cloud architecture uses Fly volumes for tenant file storage, which creates several limitations:
 
+We could enable a revolutionary user experience: **local editing (or at least view access) of cloud-stored files** while maintaining Basic Memory's existing filesystem assumptions.
+
 1. **Storage Scalability**: Fly volumes require pre-provisioning and don't auto-scale with usage
-2. **Cost Model**: Volume pricing vs object storage pricing may be less favorable at scale
-3. **Local Development**: No way for users to mount their cloud tenant files locally for real-time editing
-4. **Multi-Region**: Volumes are region-locked, limiting global deployment flexibility
-5. **Backup/Disaster Recovery**: Object storage provides better durability and replication options
+2. **Single Instance**: Volumes can only be mounted to one fly machine instance
+3. **Cost Model**: Volume pricing vs object storage pricing may be less favorable at scale
+4. **Local Development**: No way for users to mount their cloud tenant files locally for real-time editing
+5. **Multi-Region**: Volumes are region-locked, limiting global deployment flexibility
+6. **Backup/Disaster Recovery**: Object storage provides better durability and replication options
 
-The core insight is that Basic Memory requires POSIX filesystem semantics but could benefit from object storage durability and accessibility. By combining:
-- **Tigris object storage** for file persistence (via rclone mount)
-- **Turso/libSQL** for SQLite indexing (replacing local .db files)
-
-We could enable a revolutionary user experience: **local editing of cloud-stored files** while maintaining Basic Memory's existing filesystem assumptions.
+Basic Memory requires POSIX filesystem semantics but could benefit from object storage durability and accessibility. By combining:
+- **Tigris object storage and TigrisFS** for file persistence in bucket stoage via a POSIX filesystem on the tenant instance
+- **Turso/libSQL** for SQLite indexing (replacing local .db files). Sqlite on NFS volumes is disouraged. 
 
 ## What
 
@@ -36,55 +41,126 @@ This specification defines a proof-of-concept to validate the technical feasibil
 **Affected Areas:**
 - **Storage Architecture**: Replace Fly volumes with Tigris object storage
 - **Database Architecture**: Replace local SQLite with Turso remote database
-- **Container Setup**: Add rclone mounting in tenant containers
+- **Container Setup**: Add TigrisFS mounting in tenant containers
 - **Local Development**: Enable local mounting of cloud tenant data
 - **Basic Memory Core**: Validate unchanged operation over mounted filesystems
 
 **Key Components:**
-- **Tigris Storage**: S3-compatible object storage via Fly.io integration
-- **rclone NFS Mount**: Native NFS mounting without FUSE dependencies
+- **Tigris Storage**: Globally caching S3-compatible object storage via Fly.io integration
+- **TigrisFS**: Purpose-built FUSE filesystem with intelligent caching
 - **Turso Database**: Hosted libSQL for SQLite replacement
 - **Single-Tenant Model**: One bucket + one database per tenant (simplified isolation)
 
+## Architectural Overview & Key Insights
+
+### TigrisFS
+
+Unlike standard S3 mounting approaches, **TigrisFS is a purpose-built FUSE filesystem** optimized for object storage with several critical advantages:
+
+1. **Eliminates Fly Volume Limitations**
+   - No single-machine attachment constraints
+   - No pre-provisioning of storage capacity
+   - Enables horizontal scaling and zero-downtime deployments
+   - Automatic global CDN caching at Fly.io edge locations
+
+2. **Intelligent Caching Architecture**
+   - 1-4GB+ configurable memory cache for read/write operations
+   - Write-back caching for improved performance
+   - Metadata cache to reduce API calls
+   - "Close to Redis speed" for small object retrieval
+
+3. **Cost-Effective Model**
+   - Pay only for storage used and transferred
+   - No wasted capacity from over-provisioning
+   - Automatic global replication included
+   - S3 durability with CDN performance
+
+### API-Driven Architecture Eliminates File Watching Concerns
+
+**Critical Insight**: All file access (reads/writes) in basic-memory-cloud go through the API layer:
+- **MCP Tools → API**: All Basic Memory operations use FastAPI endpoints
+- **Web App → API**: Frontend uses API for all data modifications
+- **File watching is NOT required** for cloud operations, unlike local BM which uses the WatchService to monitor file changes.
+
+This means:
+- **Cloud Operations**: Manual sync after API writes is sufficient
+- **Local Development**: File watching only matters for local editing experience
+- **Performance Risk**: Dramatically reduced since we're not dependent on inotify over network filesystems
+
+### Realistic Local Access Expectations
+
+**Baseline Functionality (Guaranteed):**
+- Read-only mounting for browsing cloud files
+- Easy download/upload of entire projects
+- File copying via standard filesystem operations
+
+**Stretch Goal (Test in POC):**
+- Live editing with eventual consistency (1-5 second delays acceptable)
+- Automatic sync for local changes
+- Not required for core functionality - pure upside if it works
+
+### Production Deployment Advantages
+
+1. **Multi-Region Deployment**: Tigris handles global replication automatically
+2. **Zero-Downtime Updates**: No volume detach/attach during deployments
+3. **Tenant Migrations**: Simply update credentials, no data movement
+4. **Disaster Recovery**: Built into S3 durability model (99.999999999% durability)
+5. **Auto-Scaling**: Storage scales with usage, no capacity planning needed
+
+
 ## How (High Level)
 
-### Phase 1: Local POC Validation
-- [ ] Set up Tigris bucket with test data
-- [ ] Configure rclone NFS mount locally
-- [ ] Test Basic Memory operations over mounted filesystem
-- [ ] Measure performance characteristics and identify issues
-- [ ] Validate file watching, sync operations, and concurrent access patterns
+### POC Approach: Server-First Validation
 
-### Phase 2: Database Migration
+**Rationale**: Start with server-side TigrisFS mounting because:
+- Local access is meaningless if cloud containers can't mount TigrisFS reliably
+- Container startup and API performance are critical path blockers
+- TigrisFS compatibility with Basic Memory operations must be proven first
+- Each phase gates the next - no point testing local access if server-side fails
+
+### Phase 1: Server-Side TigrisFS Validation (Critical Foundation) ✅ COMPLETE
+- [x] Set up Tigris bucket with test data via Fly.io integration
+- [x] Create container image with TigrisFS support and dependencies
+- [x] Test TigrisFS mounting in containerized environment
+- [x] Run Basic Memory API operations over mounted TigrisFS
+- [x] Validate all filesystem operations work correctly
+- [x] Measure container startup time and resource usage
+
+**Production Validation Results**: Container successfully deployed and operated for 42+ minutes serving real MCP requests with repository queries, knowledge graph navigation, and full Basic Memory API functionality over TigrisFS-mounted storage.
+
+### Phase 2: Database Migration to Turso
 - [ ] Set up Turso account and test database
 - [ ] Modify Basic Memory to accept external DATABASE_URL
-- [ ] Test all operations with remote SQLite via Turso
+- [ ] Test all MCP tools with remote SQLite via Turso
 - [ ] Validate performance and functionality parity
+- [ ] Test API write → manual sync workflow in container
 
-### Phase 3: Container Integration
-- [ ] Create container image with rclone + NFS support
-- [ ] Implement tenant-specific credential management
-- [ ] Test container startup with automatic mounting
+### Phase 3: Production Container Integration
+- [ ] Implement tenant-specific credential management for buckets
+- [x] Test container startup with automatic TigrisFS mounting
 - [ ] Validate isolation between tenant containers
+- [ ] Test API operations under realistic load
+- [ ] Measure performance vs current Fly volume setup
 
-### Phase 4: Local Access Validation
-- [ ] Test local rclone mounting of tenant data
-- [ ] Validate real-time file editing experience
-- [ ] Test conflict resolution and sync behavior
+### Phase 4: Local Access Validation (Bonus Feature)
+- [ ] Test local TigrisFS mounting of tenant data
+- [ ] Validate read-only access for browsing/downloading
+- [ ] Test file copying and upload workflows
 - [ ] Measure latency impact on user experience
+- [ ] Test live editing if file watching works (stretch goal)
 
 ### Architecture Overview
 ```
 Local Development:
 ┌─────────────────┐    ┌─────────────────┐    ┌─────────────────┐
-│ Local rclone    │───▶│ Tigris Bucket   │◀───│ Tenant Container│
-│ NFS Mount       │    │ (S3 storage)    │    │ rclone mount    │
+│ Local TigrisFS  │───▶│ Tigris Bucket   │◀───│ Tenant Container│
+│ Mount           │    │ (Global CDN)    │    │ TigrisFS mount  │
 └─────────────────┘    └─────────────────┘    └─────────────────┘
          │                                              │
          ▼                                              ▼
 ┌─────────────────┐                            ┌─────────────────┐
 │ Basic Memory    │                            │ Basic Memory    │
-│ (local files)   │                            │ (mounted files) │
+│ (local files)   │                            │ API + mounted   │
 └─────────────────┘                            └─────────────────┘
          │                                              │
          ▼                                              ▼
@@ -92,102 +168,157 @@ Local Development:
 │ Turso Database  │◀───────────────────────────│ Turso Database  │
 │ (shared index)  │                            │ (shared index)  │
 └─────────────────┘                            └─────────────────┘
+
+Flow: API writes → Manual sync → Index update
+Local: File watching (if available) → Auto sync
 ```
 
 ## How to Evaluate
 
 ### Success Criteria
-- [ ] **Filesystem Compatibility**: Basic Memory operates without modification over rclone-mounted Tigris storage
-- [ ] **Performance Acceptable**: File operations complete within 2x local filesystem latency
+- [x] **Filesystem Compatibility**: Basic Memory operates without modification over TigrisFS-mounted storage
+- [x] **Performance Acceptable**: API-driven operations perform within acceptable latency (target: <500ms for typical operations)
 - [ ] **Database Functionality**: All Basic Memory features work with Turso remote SQLite
-- [ ] **Container Reliability**: Tenant containers start successfully with automatic mounting
-- [ ] **Local Access**: Users can mount and edit cloud files locally with real-time sync
-- [ ] **Data Isolation**: Tenant data remains properly isolated using bucket/database separation
+- [x] **Container Reliability**: Tenant containers start successfully with automatic TigrisFS mounting
+- [ ] **Local Access Baseline**: Users can mount cloud files locally for read-only browsing and file copying
+- [x] **Data Isolation**: Tenant data remains properly isolated using bucket/database separation
+- [ ] **Local Access Stretch**: Live editing with eventual sync (1-5 second delays acceptable)
 
 ### Testing Procedure
-1. **Local Filesystem Test**:
-   ```bash
-   # Mount Tigris bucket locally
-   rclone nfsmount tigris:test-bucket ~/tigris-test --vfs-cache-mode writes
 
-   # Run Basic Memory operations
-   cd ~/tigris-test && basic-memory sync --watch
-   # Test: create notes, search, file watching, bulk operations
+#### Phase 1: Server-Side Foundation Testing
+1. **Container TigrisFS Test**:
+   ```dockerfile
+   # Test container with TigrisFS mounting
+   FROM python:3.12
+   RUN apt-get update && apt-get install -y tigrisfs
+
+   # Test startup script
+   #!/bin/bash
+   tigrisfs --memory-limit 2048 $TIGRIS_BUCKET /app/data --daemon
+   cd /app/data && basic-memory sync
+   basic-memory-api --data-dir /app/data
    ```
 
-2. **Database Migration Test**:
+2. **API Operations Validation**:
    ```bash
-   # Configure Turso connection
+   # Test all MCP operations over TigrisFS
+   curl -X POST /api/write_note -d '{"title":"test","content":"content"}'
+   curl -X GET /api/read_note/test
+   curl -X GET /api/search_notes?q=content
+   # Measure: response times, error rates, data consistency
+   ```
+
+#### Phase 2: Database Integration Testing
+3. **Turso Integration Test**:
+   ```bash
+   # Configure Turso connection in container
    export DATABASE_URL="libsql://test-db.turso.io?authToken=..."
 
    # Test all MCP tools with remote database
    basic-memory tools # Test each tool functionality
+   # Test API write → manual sync workflow
    ```
 
-3. **Container Integration Test**:
-   ```dockerfile
-   # Test container with rclone mounting
-   FROM python:3.12
-   RUN apt-get update && apt-get install -y rclone nfs-common
-   # ... test startup and mounting process
-   ```
-
+#### Phase 3: Production Readiness Testing
 4. **Performance Benchmarking**:
-   - File creation/read/write operations (target: <2x local latency)
-   - Search query performance (target: comparable to local SQLite)
-   - File watching responsiveness (target: events within 1-2 seconds)
-   - Concurrent operation handling
+   - Container startup time with TigrisFS mounting
+   - API operation response times (target: <500ms for typical operations)
+   - Search query performance with Turso (target: comparable to local SQLite)
+   - TigrisFS cache hit rates and memory usage
+   - Concurrent tenant isolation
+
+#### Phase 4: Local Access Testing (If Phase 1-3 Succeed)
+5. **Local Access Validation**:
+   ```bash
+   # Test read-only access
+   tigrisfs tenant-bucket ~/local-tenant
+   ls -la ~/local-tenant  # Browse files
+   cp ~/local-tenant/notes/* ~/backup/  # Copy files
+
+   # Test file watching (stretch goal)
+   echo "test" > ~/local-tenant/test.md
+   # Check if changes sync to cloud
+   ```
+
+### Go/No-Go Criteria by Phase
+- **Phase 1**: Container must start successfully and serve API requests over TigrisFS
+- **Phase 2**: All MCP tools must work with Turso with <2x latency increase
+- **Phase 3**: Performance must be within 50% of current Fly volume setup
+- **Phase 4**: Local mounting must work reliably for read-only access
 
 ### Risk Assessment
-**High Risk Items**:
-- [ ] NFS-over-S3 performance may be insufficient for real-time operations
-- [ ] File watching (`inotify`) over NFS may be unreliable
-- [ ] Network interruptions could cause filesystem errors
-- [ ] Concurrent access patterns might hit S3 rate limits
+**Moderate Risk Items (Mitigated by API-First Architecture)**:
+- [ ] TigrisFS performance for local access may have higher latency than local filesystem
+- [ ] File watching (`inotify`) over FUSE may be unreliable for local development
+- [ ] Network interruptions could cause filesystem errors during local editing
+- [ ] Write-back caching could cause data loss if container crashes during flush
+
+**Low Risk Items (API-First Eliminates)**:
+- [ ] ~~Real-time file watching~~ - Not required for cloud operations
+- [ ] ~~Concurrent write consistency~~ - Single-tenant model with API coordination
+- [ ] ~~S3 rate limits~~ - TigrisFS intelligent caching handles this
 
 **Mitigation Strategies**:
-- Comprehensive performance testing before committing to architecture
-- Fallback plan to S3-native storage backend if filesystem approach fails
-- Extensive error handling and retry logic for network issues
+- **Performance**: Comprehensive benchmarking with realistic workloads
+- **Reliability**: Graceful degradation to read-only local access if live editing fails
+- **Data Safety**: Regular sync intervals and write-through mode for critical operations
+- **Fallback**: Keep Fly volumes as backup deployment option
 
 ### Metrics to Track
-- **Latency**: File operation response times (read/write/watch)
-- **Reliability**: Success rate of file operations over time
-- **Throughput**: Concurrent file operations and search queries
-- **User Experience**: Perceived performance for local mounting use case
+- **API Latency**: Response times for MCP tools and web operations
+- **Cache Effectiveness**: TigrisFS cache hit rates and memory usage
+- **Local Access Performance**: File browsing and copying speeds
+- **Reliability**: Success rate of mount operations and data consistency
+- **Cost**: Storage usage, API calls, and network transfer costs vs current volumes
 
 ## Notes
 
 ### Key Architectural Decisions
 - **Single tenant per bucket/database**: Simplifies isolation and credential management
 - **Maintain POSIX compatibility**: Preserve Basic Memory's existing filesystem assumptions
-- **NFS over FUSE**: Better compatibility and performance characteristics
+- **TigrisFS over rclone**: Purpose-built for object storage with intelligent caching
 - **Turso for SQLite**: Leverages specialized remote SQLite expertise
+- **API-first approach**: Eliminates file watching dependency for cloud operations
 
 ### Alternative Approaches Considered
 - **S3-native storage backend**: Would require Basic Memory architecture changes
 - **Hybrid approach**: Local files + cloud sync (adds complexity)
-- **FUSE mounting**: More platform dependencies and kernel requirements
+- **Standard rclone mounting**: Less optimized than TigrisFS for object storage workloads
+- **Keep Fly volumes**: Maintains current limitations but proven reliability
 
 ### Integration Points
 - [ ] Fly.io Tigris integration for bucket provisioning
 - [ ] Turso account setup and database provisioning
-- [ ] Container image modifications for rclone support
+- [ ] Container image modifications for TigrisFS support
 - [ ] Credential management for tenant isolation
+- [ ] API modification for manual sync triggers
+- [ ] Local client setup documentation for TigrisFS mounting
 
 ## Observations
 
 - [architecture] Tigris/Turso split cleanly separates file storage from indexing concerns #storage-separation
+- [breakthrough] API-first architecture eliminates file watching dependency for cloud operations #api-first-advantage
 - [user-experience] Local mounting of cloud files could be revolutionary for knowledge management #local-cloud-hybrid
 - [compatibility] Maintaining POSIX filesystem assumptions preserves Basic Memory's local/cloud compatibility #architecture-preservation
 - [simplification] Single tenant per bucket eliminates complex multi-tenancy in storage layer #tenant-isolation
-- [risk] NFS-over-S3 performance characteristics are unproven for real-time operations #performance-risk
+- [performance] TigrisFS intelligent caching could provide near-local performance for common operations #tigrisfs-advantage
+- [deployment] Zero-downtime updates become trivial without volume constraints #deployment-simplification
 - [benefit] Object storage pricing model could be more favorable than volume pricing #cost-optimization
-- [innovation] Real-time local editing of cloud-stored files addresses major SaaS limitation #competitive-advantage
+- [innovation] Read-only local access alone would address major SaaS limitation #competitive-advantage
+- [risk-mitigation] API-driven sync reduces performance requirements vs real-time file watching #risk-reduction
 
 ## Relations
 
 - implements [[SPEC-6 Explicit Project Parameter Architecture]]
 - requires [[Fly.io Tigris Integration]]
 - enables [[Local Cloud File Access]]
-- alternative_to [[Fly Volume Storage]]
+- alternative_to [[Fly Volume Storage]]
+
+## Links
+- https://fly.io/hello/tigris
+- https://fly.io/docs/tigris/
+- https://www.tigrisdata.com/docs/sdks/fly/data-migration-with-flyctl/
+- https://www.tigrisdata.com/docs/training/tigrisfs/
+- https://www.tigrisdata.com/blog/tigris-filesystem/
+- https://www.tigrisdata.com/docs/quickstarts/rclone/

specs/SPEC-9 Signed Header Tenant Information.md

@@ -0,0 +1,196 @@
+---
+title: 'SPEC-9: Signed Header Tenant Information'
+type: spec
+permalink: specs/spec-9-signed-header-tenant-information
+tags:
+- authentication
+- tenant-isolation
+- proxy
+- security
+- mcp
+---
+
+# SPEC-9: Signed Header Tenant Information
+
+## Why
+
+WorkOS JWT templates don't work with MCP's dynamic client registration requirement, preventing us from getting tenant information directly in JWT tokens. We need an alternative secure method to pass tenant context from the Cloud Proxy Service to tenant instances.
+
+**Problem Context:**
+- MCP spec requires dynamic client registration
+- WorkOS JWT templates only apply to statically configured clients
+- Without tenant information, we can't properly route requests or isolate tenant data
+- Current JWT tokens only contain standard OIDC claims (sub, email, etc.)
+
+**Affected Areas:**
+- Cloud Proxy Service (`apps/cloud`) - request forwarding
+- Tenant API instances (`apps/api`) - tenant context validation
+- MCP Gateway (`apps/mcp`) - authentication flow
+- Overall tenant isolation security model
+
+## What
+
+Implement HMAC-signed headers that the Cloud Proxy Service adds when forwarding requests to tenant instances. This provides secure, tamper-proof tenant information without relying on JWT custom claims.
+
+**Components:**
+- Header signing utility in Cloud Proxy Service
+- Header validation middleware in Tenant API instances
+- Shared secret configuration across services
+- Fallback mechanisms for development and error cases
+
+## How (High Level)
+
+### 1. Header Format
+Add these signed headers to all proxied requests:
+```
+X-BM-Tenant-ID: {tenant_id}
+X-BM-Timestamp: {unix_timestamp}
+X-BM-Signature: {hmac_sha256_signature}
+```
+
+### 2. Signature Algorithm
+```python
+# Canonical message format
+message = f"{tenant_id}:{timestamp}"
+
+# HMAC-SHA256 signature
+signature = hmac.new(
+    key=shared_secret.encode('utf-8'),
+    msg=message.encode('utf-8'),
+    digestmod=hashlib.sha256
+).hexdigest()
+```
+
+### 3. Implementation Flow
+
+#### Cloud Proxy Service (`apps/cloud`)
+1. Extract `tenant_id` from authenticated user profile
+2. Generate timestamp and canonical message
+3. Sign message with shared secret
+4. Add headers to request before forwarding to tenant instance
+
+#### Tenant API Instances (`apps/api`)
+1. Middleware validates headers on all incoming requests
+2. Extract tenant_id, timestamp from headers
+3. Verify timestamp is within acceptable window (5 minutes)
+4. Recompute signature and compare in constant time
+5. If valid, make tenant context available to Basic Memory tools
+
+### 4. Security Properties
+- **Authenticity**: Only services with shared secret can create valid signatures
+- **Integrity**: Header tampering invalidates signature
+- **Replay Protection**: Timestamp prevents reuse of old signatures
+- **Non-repudiation**: Each request is cryptographically tied to specific tenant
+
+### 5. Configuration
+```bash
+# Shared across Cloud Proxy and Tenant instances
+BM_TENANT_HEADER_SECRET=randomly-generated-256-bit-secret
+
+# Tenant API configuration
+BM_TENANT_HEADER_VALIDATION=true  # true (production) | false (dev only)
+```
+
+## How to Evaluate
+
+### Unit Tests
+- [ ] Header signing utility generates correct signatures
+- [ ] Header validation correctly accepts/rejects signatures
+- [ ] Timestamp validation within acceptable windows
+- [ ] Constant-time signature comparison prevents timing attacks
+
+### Integration Tests
+- [ ] End-to-end request flow from MCP client → proxy → tenant
+- [ ] Tenant isolation verified with signed headers
+- [ ] Error handling for missing/invalid headers
+- [ ] Disabled validation in development environment
+
+### Security Validation
+- [ ] Shared secret rotation procedure
+- [ ] Header tampering detection
+- [ ] Clock skew tolerance testing
+- [ ] Performance impact measurement
+
+### Production Readiness
+- [ ] Logging and monitoring of header validation
+- [ ] Graceful degradation for header validation failures
+- [ ] Documentation for secret management
+- [ ] Deployment configuration templates
+
+## Implementation Notes
+
+### Shared Secret Management
+- Generate cryptographically secure 256-bit secret
+- Same secret deployed to Cloud Proxy and all Tenant instances
+- Consider secret rotation strategy for production
+
+### Error Handling
+```python
+# Strict mode (production)
+if not validate_headers(request):
+    raise HTTPException(status_code=401, detail="Invalid tenant headers")
+
+# Fallback mode (development)
+if not validate_headers(request):
+    logger.warning("Invalid headers, falling back to default tenant")
+    tenant_id = "default"
+```
+
+### Performance Considerations
+- HMAC-SHA256 computation is fast (~microseconds)
+- Headers add ~200 bytes to each request
+- Validation happens once per request in middleware
+
+## Benefits
+
+✅ **Works with MCP dynamic client registration** - No dependency on JWT custom claims
+✅ **Simple and reliable** - Standard HMAC signature approach
+✅ **Secure by design** - Cryptographic authenticity and integrity
+✅ **Infrastructure controlled** - No external service dependencies
+✅ **Easy to implement** - Clear signature algorithm and validation
+
+## Trade-offs
+
+⚠️ **Shared secret management** - Need secure distribution and rotation
+⚠️ **Clock synchronization** - Timestamp validation requires reasonably synced clocks
+⚠️ **Header visibility** - Headers visible in logs (tenant_id not sensitive)
+⚠️ **Additional complexity** - More moving parts in proxy forwarding
+
+## Implementation Tasks
+
+### Cloud Service (Header Signing)
+- [ ] Create `utils/header_signing.py` with HMAC-SHA256 signing function
+- [ ] Add `bm_tenant_header_secret` to Cloud service configuration
+- [ ] Update `ProxyService.forward_request()` to call signing utility
+- [ ] Add signed headers (X-BM-Tenant-ID, X-BM-Timestamp, X-BM-Signature)
+
+### Tenant API (Header Validation)
+- [ ] Create `utils/header_validation.py` with signature verification
+- [ ] Add `bm_tenant_header_secret` to API service configuration
+- [ ] Create `TenantHeaderValidationMiddleware` class
+- [ ] Add middleware to FastAPI app (before other middleware)
+- [ ] Skip validation for `/health` endpoint
+- [ ] Store validated tenant_id in request.state
+
+### Testing
+- [ ] Unit test for header signing utility
+- [ ] Unit test for header validation utility
+- [ ] Integration test for proxy → tenant flow
+- [ ] Test invalid/missing header handling
+- [ ] Test timestamp window validation
+- [ ] Test signature tampering detection
+
+### Configuration & Deployment
+- [ ] Update `.env.example` with BM_TENANT_HEADER_SECRET
+- [ ] Generate secure 256-bit secret for production
+- [ ] Update Fly.io secrets for both services
+- [ ] Document secret rotation procedure
+
+## Status
+
+- [x] **Specification Complete** - Design finalized and documented
+- [ ] **Implementation Started** - Header signing utility development
+- [ ] **Cloud Proxy Updated** - ProxyService adds signed headers
+- [ ] **Tenant Validation Added** - Middleware validates headers
+- [ ] **Testing Complete** - All validation criteria met
+- [ ] **Production Deployed** - Live with tenant isolation via headers

src/basic_memory/__init__.py

@@ -1,7 +1,7 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""
 
 # Package version - updated by release automation
-__version__ = "0.15.1"
+__version__ = "0.16.2"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

src/basic_memory/alembic/env.py

@@ -8,7 +8,7 @@ from sqlalchemy import pool
 
 from alembic import context
 
-from basic_memory.config import ConfigManager
+from basic_memory.config import ConfigManager, DatabaseBackend
 
 # set config.env to "test" for pytest to prevent logging to file in utils.setup_logging()
 os.environ["BASIC_MEMORY_ENV"] = "test"
@@ -20,12 +20,28 @@ from basic_memory.models import Base  # noqa: E402
 # access to the values within the .ini file in use.
 config = context.config
 
+# Load app config - this will read environment variables (BASIC_MEMORY_DATABASE_BACKEND, etc.)
+# due to Pydantic's env_prefix="BASIC_MEMORY_" setting
 app_config = ConfigManager().config
-# Set the SQLAlchemy URL from our app config
-sqlalchemy_url = f"sqlite:///{app_config.database_path}"
-config.set_main_option("sqlalchemy.url", sqlalchemy_url)
 
-# print(f"Using SQLAlchemy URL: {sqlalchemy_url}")
+# Set the SQLAlchemy URL based on database backend configuration
+# If the URL is already set in config (e.g., from run_migrations), use that
+# Otherwise, get it from app config
+# Note: alembic.ini has a placeholder URL "driver://user:pass@localhost/dbname" that we need to override
+current_url = config.get_main_option("sqlalchemy.url")
+if not current_url or current_url == "driver://user:pass@localhost/dbname":
+    from basic_memory.db import DatabaseType
+
+    sqlalchemy_url = DatabaseType.get_db_url(
+        app_config.database_path, DatabaseType.FILESYSTEM, app_config
+    )
+
+    # For Postgres, Alembic needs synchronous driver (psycopg2), not async (asyncpg)
+    if app_config.database_backend == DatabaseBackend.POSTGRES:
+        # Convert asyncpg URL to psycopg2 URL for Alembic
+        sqlalchemy_url = sqlalchemy_url.replace("postgresql+asyncpg://", "postgresql://")
+
+    config.set_main_option("sqlalchemy.url", sqlalchemy_url)
 
 # Interpret the config file for Python logging.
 if config.config_file_name is not None:

src/basic_memory/alembic/versions/314f1ea54dc4_add_postgres_full_text_search_support_.py

@@ -0,0 +1,131 @@
+"""Add Postgres full-text search support with tsvector and GIN indexes
+
+Revision ID: 314f1ea54dc4
+Revises: e7e1f4367280
+Create Date: 2025-11-15 18:05:01.025405
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "314f1ea54dc4"
+down_revision: Union[str, None] = "e7e1f4367280"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Add PostgreSQL full-text search support.
+
+    This migration:
+    1. Creates search_index table for Postgres (SQLite uses FTS5 virtual table)
+    2. Adds generated tsvector column for full-text search
+    3. Creates GIN index on the tsvector column for fast text queries
+    4. Creates GIN index on metadata JSONB column for fast containment queries
+
+    Note: These changes only apply to Postgres. SQLite continues to use FTS5 virtual tables.
+    """
+    # Check if we're using Postgres
+    connection = op.get_bind()
+    if connection.dialect.name == "postgresql":
+        # Create search_index table for Postgres
+        # For SQLite, this is a FTS5 virtual table created elsewhere
+        from sqlalchemy.dialects.postgresql import JSONB
+
+        op.create_table(
+            "search_index",
+            sa.Column("id", sa.Integer(), nullable=False),  # Entity IDs are integers
+            sa.Column("project_id", sa.Integer(), nullable=False),  # Multi-tenant isolation
+            sa.Column("title", sa.Text(), nullable=True),
+            sa.Column("content_stems", sa.Text(), nullable=True),
+            sa.Column("content_snippet", sa.Text(), nullable=True),
+            sa.Column("permalink", sa.String(), nullable=True),  # Nullable for non-markdown files
+            sa.Column("file_path", sa.String(), nullable=True),
+            sa.Column("type", sa.String(), nullable=True),
+            sa.Column("from_id", sa.Integer(), nullable=True),  # Relation IDs are integers
+            sa.Column("to_id", sa.Integer(), nullable=True),  # Relation IDs are integers
+            sa.Column("relation_type", sa.String(), nullable=True),
+            sa.Column("entity_id", sa.Integer(), nullable=True),  # Entity IDs are integers
+            sa.Column("category", sa.String(), nullable=True),
+            sa.Column("metadata", JSONB(), nullable=True),  # Use JSONB for Postgres
+            sa.Column("created_at", sa.DateTime(timezone=True), nullable=True),
+            sa.Column("updated_at", sa.DateTime(timezone=True), nullable=True),
+            sa.PrimaryKeyConstraint(
+                "id", "type", "project_id"
+            ),  # Composite key: id can repeat across types
+            sa.ForeignKeyConstraint(
+                ["project_id"],
+                ["project.id"],
+                name="fk_search_index_project_id",
+                ondelete="CASCADE",
+            ),
+            if_not_exists=True,
+        )
+
+        # Create index on project_id for efficient multi-tenant queries
+        op.create_index(
+            "ix_search_index_project_id",
+            "search_index",
+            ["project_id"],
+            unique=False,
+        )
+
+        # Create unique partial index on permalink for markdown files
+        # Non-markdown files don't have permalinks, so we use a partial index
+        op.execute("""
+            CREATE UNIQUE INDEX uix_search_index_permalink_project
+            ON search_index (permalink, project_id)
+            WHERE permalink IS NOT NULL
+        """)
+
+        # Add tsvector column as a GENERATED ALWAYS column
+        # This automatically updates when title or content_stems change
+        op.execute("""
+            ALTER TABLE search_index
+            ADD COLUMN textsearchable_index_col tsvector
+            GENERATED ALWAYS AS (
+                to_tsvector('english',
+                    coalesce(title, '') || ' ' ||
+                    coalesce(content_stems, '')
+                )
+            ) STORED
+        """)
+
+        # Create GIN index on tsvector column for fast full-text search
+        op.create_index(
+            "idx_search_index_fts",
+            "search_index",
+            ["textsearchable_index_col"],
+            unique=False,
+            postgresql_using="gin",
+        )
+
+        # Create GIN index on metadata JSONB for fast containment queries
+        # Using jsonb_path_ops for smaller index size and better performance
+        op.execute("""
+            CREATE INDEX idx_search_index_metadata_gin
+            ON search_index
+            USING GIN (metadata jsonb_path_ops)
+        """)
+
+
+def downgrade() -> None:
+    """Remove PostgreSQL full-text search support."""
+    connection = op.get_bind()
+    if connection.dialect.name == "postgresql":
+        # Drop indexes first
+        op.execute("DROP INDEX IF EXISTS idx_search_index_metadata_gin")
+        op.drop_index("idx_search_index_fts", table_name="search_index")
+        op.execute("DROP INDEX IF EXISTS uix_search_index_permalink_project")
+        op.drop_index("ix_search_index_project_id", table_name="search_index")
+
+        # Drop the generated column
+        op.execute("ALTER TABLE search_index DROP COLUMN IF EXISTS textsearchable_index_col")
+
+        # Drop the search_index table
+        op.drop_table("search_index")

src/basic_memory/alembic/versions/5fe1ab1ccebe_add_projects_table.py

@@ -21,6 +21,12 @@ depends_on: Union[str, Sequence[str], None] = None
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+
+    # SQLite FTS5 virtual table handling is SQLite-specific
+    # For Postgres, search_index is a regular table managed by ORM
+    connection = op.get_bind()
+    is_sqlite = connection.dialect.name == "sqlite"
+
     op.create_table(
         "project",
         sa.Column("id", sa.Integer(), nullable=False),
@@ -55,7 +61,9 @@ def upgrade() -> None:
         batch_op.add_column(sa.Column("project_id", sa.Integer(), nullable=False))
         batch_op.drop_index(
             "uix_entity_permalink",
-            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL"),
+            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL")
+            if is_sqlite
+            else None,
         )
         batch_op.drop_index("ix_entity_file_path")
         batch_op.create_index(batch_op.f("ix_entity_file_path"), ["file_path"], unique=False)
@@ -67,12 +75,16 @@ def upgrade() -> None:
             "uix_entity_permalink_project",
             ["permalink", "project_id"],
             unique=True,
-            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL"),
+            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL")
+            if is_sqlite
+            else None,
         )
         batch_op.create_foreign_key("fk_entity_project_id", "project", ["project_id"], ["id"])
 
     # drop the search index table. it will be recreated
-    op.drop_table("search_index")
+    # Only drop for SQLite - Postgres uses regular table managed by ORM
+    if is_sqlite:
+        op.drop_table("search_index")
 
     # ### end Alembic commands ###
 

src/basic_memory/alembic/versions/647e7a75e2cd_project_constraint_fix.py

@@ -25,43 +25,51 @@ def upgrade() -> None:
     The UNIQUE constraint prevents multiple projects from having is_default=FALSE,
     which breaks project creation when the service sets is_default=False.
 
-    Since SQLite doesn't support dropping specific constraints easily, we'll
-    recreate the table without the problematic constraint.
+    SQLite: Recreate the table without the constraint (no ALTER TABLE support)
+    Postgres: Use ALTER TABLE to drop the constraint directly
     """
-    # For SQLite, we need to recreate the table without the UNIQUE constraint
-    # Create a new table without the UNIQUE constraint on is_default
-    op.create_table(
-        "project_new",
-        sa.Column("id", sa.Integer(), nullable=False),
-        sa.Column("name", sa.String(), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("permalink", sa.String(), nullable=False),
-        sa.Column("path", sa.String(), nullable=False),
-        sa.Column("is_active", sa.Boolean(), nullable=False),
-        sa.Column("is_default", sa.Boolean(), nullable=True),  # No UNIQUE constraint!
-        sa.Column("created_at", sa.DateTime(), nullable=False),
-        sa.Column("updated_at", sa.DateTime(), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("name"),
-        sa.UniqueConstraint("permalink"),
-    )
+    connection = op.get_bind()
+    is_sqlite = connection.dialect.name == "sqlite"
 
-    # Copy data from old table to new table
-    op.execute("INSERT INTO project_new SELECT * FROM project")
+    if is_sqlite:
+        # For SQLite, we need to recreate the table without the UNIQUE constraint
+        # Create a new table without the UNIQUE constraint on is_default
+        op.create_table(
+            "project_new",
+            sa.Column("id", sa.Integer(), nullable=False),
+            sa.Column("name", sa.String(), nullable=False),
+            sa.Column("description", sa.Text(), nullable=True),
+            sa.Column("permalink", sa.String(), nullable=False),
+            sa.Column("path", sa.String(), nullable=False),
+            sa.Column("is_active", sa.Boolean(), nullable=False),
+            sa.Column("is_default", sa.Boolean(), nullable=True),  # No UNIQUE constraint!
+            sa.Column("created_at", sa.DateTime(), nullable=False),
+            sa.Column("updated_at", sa.DateTime(), nullable=False),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint("name"),
+            sa.UniqueConstraint("permalink"),
+        )
 
-    # Drop the old table
-    op.drop_table("project")
+        # Copy data from old table to new table
+        op.execute("INSERT INTO project_new SELECT * FROM project")
 
-    # Rename the new table
-    op.rename_table("project_new", "project")
+        # Drop the old table
+        op.drop_table("project")
 
-    # Recreate the indexes
-    with op.batch_alter_table("project", schema=None) as batch_op:
-        batch_op.create_index("ix_project_created_at", ["created_at"], unique=False)
-        batch_op.create_index("ix_project_name", ["name"], unique=True)
-        batch_op.create_index("ix_project_path", ["path"], unique=False)
-        batch_op.create_index("ix_project_permalink", ["permalink"], unique=True)
-        batch_op.create_index("ix_project_updated_at", ["updated_at"], unique=False)
+        # Rename the new table
+        op.rename_table("project_new", "project")
+
+        # Recreate the indexes
+        with op.batch_alter_table("project", schema=None) as batch_op:
+            batch_op.create_index("ix_project_created_at", ["created_at"], unique=False)
+            batch_op.create_index("ix_project_name", ["name"], unique=True)
+            batch_op.create_index("ix_project_path", ["path"], unique=False)
+            batch_op.create_index("ix_project_permalink", ["permalink"], unique=True)
+            batch_op.create_index("ix_project_updated_at", ["updated_at"], unique=False)
+    else:
+        # For Postgres, we can simply drop the constraint
+        with op.batch_alter_table("project", schema=None) as batch_op:
+            batch_op.drop_constraint("project_is_default_key", type_="unique")
 
 
 def downgrade() -> None:

src/basic_memory/alembic/versions/9d9c1cb7d8f5_add_mtime_and_size_columns_to_entity_.py

@@ -0,0 +1,49 @@
+"""Add mtime and size columns to Entity for sync optimization
+
+Revision ID: 9d9c1cb7d8f5
+Revises: a1b2c3d4e5f6
+Create Date: 2025-10-20 05:07:55.173849
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "9d9c1cb7d8f5"
+down_revision: Union[str, None] = "a1b2c3d4e5f6"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        batch_op.add_column(sa.Column("mtime", sa.Float(), nullable=True))
+        batch_op.add_column(sa.Column("size", sa.Integer(), nullable=True))
+        batch_op.drop_constraint(batch_op.f("fk_entity_project_id"), type_="foreignkey")
+        batch_op.create_foreign_key(
+            batch_op.f("fk_entity_project_id"), "project", ["project_id"], ["id"]
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        batch_op.drop_constraint(batch_op.f("fk_entity_project_id"), type_="foreignkey")
+        batch_op.create_foreign_key(
+            batch_op.f("fk_entity_project_id"),
+            "project",
+            ["project_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+        batch_op.drop_column("size")
+        batch_op.drop_column("mtime")
+
+    # ### end Alembic commands ###

src/basic_memory/alembic/versions/cc7172b46608_update_search_index_schema.py

@@ -21,6 +21,12 @@ depends_on: Union[str, Sequence[str], None] = None
 def upgrade() -> None:
     """Upgrade database schema to use new search index with content_stems and content_snippet."""
 
+    # This migration is SQLite-specific (FTS5 virtual tables)
+    # For Postgres, the search_index table is created via ORM models
+    connection = op.get_bind()
+    if connection.dialect.name != "sqlite":
+        return
+
     # First, drop the existing search_index table
     op.execute("DROP TABLE IF EXISTS search_index")
 
@@ -59,6 +65,13 @@ def upgrade() -> None:
 
 def downgrade() -> None:
     """Downgrade database schema to use old search index."""
+
+    # This migration is SQLite-specific (FTS5 virtual tables)
+    # For Postgres, the search_index table is managed via ORM models
+    connection = op.get_bind()
+    if connection.dialect.name != "sqlite":
+        return
+
     # Drop the updated search_index table
     op.execute("DROP TABLE IF EXISTS search_index")
 

src/basic_memory/alembic/versions/e7e1f4367280_add_scan_watermark_tracking_to_project.py

@@ -0,0 +1,37 @@
+"""Add scan watermark tracking to Project
+
+Revision ID: e7e1f4367280
+Revises: 9d9c1cb7d8f5
+Create Date: 2025-10-20 16:42:46.625075
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "e7e1f4367280"
+down_revision: Union[str, None] = "9d9c1cb7d8f5"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("project", schema=None) as batch_op:
+        batch_op.add_column(sa.Column("last_scan_timestamp", sa.Float(), nullable=True))
+        batch_op.add_column(sa.Column("last_file_count", sa.Integer(), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("project", schema=None) as batch_op:
+        batch_op.drop_column("last_file_count")
+        batch_op.drop_column("last_scan_timestamp")
+
+    # ### end Alembic commands ###

src/basic_memory/api/routers/project_router.py

@@ -1,7 +1,7 @@
 """Router for project management."""
 
 import os
-from fastapi import APIRouter, HTTPException, Path, Body, BackgroundTasks
+from fastapi import APIRouter, HTTPException, Path, Body, BackgroundTasks, Response, Query
 from typing import Optional
 from loguru import logger
 
@@ -18,6 +18,7 @@ from basic_memory.schemas.project_info import (
     ProjectInfoRequest,
     ProjectStatusResponse,
 )
+from basic_memory.utils import normalize_project_path
 
 # Router for resources in a specific project
 # The ProjectPathDep is used in the path as a prefix, so the request path is like /{project}/project/info
@@ -50,7 +51,7 @@ async def get_project(
 
     return ProjectItem(
         name=found_project.name,
-        path=found_project.path,
+        path=normalize_project_path(found_project.path),
         is_default=found_project.is_default or False,
     )
 
@@ -109,6 +110,10 @@ async def sync_project(
     background_tasks: BackgroundTasks,
     sync_service: SyncServiceDep,
     project_config: ProjectConfigDep,
+    force_full: bool = Query(
+        False, description="Force full scan, bypassing watermark optimization"
+    ),
+    run_in_background: bool = Query(True, description="Run in background"),
 ):
     """Force project filesystem sync to database.
 
@@ -118,17 +123,32 @@ async def sync_project(
         background_tasks: FastAPI background tasks
         sync_service: Sync service for this project
         project_config: Project configuration
+        force_full: If True, force a full scan even if watermark exists
+        run_in_background: If True, run sync in background and return immediately
 
     Returns:
-        Response confirming sync was initiated
+        Response confirming sync was initiated (background) or SyncReportResponse (foreground)
     """
-    background_tasks.add_task(sync_service.sync, project_config.home, project_config.name)
-    logger.info(f"Filesystem sync initiated for project: {project_config.name}")
+    if run_in_background:
+        background_tasks.add_task(
+            sync_service.sync, project_config.home, project_config.name, force_full=force_full
+        )
+        logger.info(
+            f"Filesystem sync initiated for project: {project_config.name} (force_full={force_full})"
+        )
 
-    return {
-        "status": "sync_started",
-        "message": f"Filesystem sync initiated for project '{project_config.name}'",
-    }
+        return {
+            "status": "sync_started",
+            "message": f"Filesystem sync initiated for project '{project_config.name}'",
+        }
+    else:
+        report = await sync_service.sync(
+            project_config.home, project_config.name, force_full=force_full
+        )
+        logger.info(
+            f"Filesystem sync completed for project: {project_config.name} (force_full={force_full})"
+        )
+        return SyncReportResponse.from_sync_report(report)
 
 
 @project_router.post("/status", response_model=SyncReportResponse)
@@ -167,7 +187,7 @@ async def list_projects(
     project_items = [
         ProjectItem(
             name=project.name,
-            path=project.path,
+            path=normalize_project_path(project.path),
             is_default=project.is_default or False,
         )
         for project in projects
@@ -180,8 +200,9 @@ async def list_projects(
 
 
 # Add a new project
-@project_resource_router.post("/projects", response_model=ProjectStatusResponse)
+@project_resource_router.post("/projects", response_model=ProjectStatusResponse, status_code=201)
 async def add_project(
+    response: Response,
     project_data: ProjectInfoRequest,
     project_service: ProjectServiceDep,
 ) -> ProjectStatusResponse:
@@ -193,6 +214,36 @@ async def add_project(
     Returns:
         Response confirming the project was added
     """
+    # Check if project already exists before attempting to add
+    existing_project = await project_service.get_project(project_data.name)
+    if existing_project:
+        # Project exists - check if paths match for true idempotency
+        # Normalize paths for comparison (resolve symlinks, etc.)
+        from pathlib import Path
+
+        requested_path = Path(project_data.path).resolve()
+        existing_path = Path(existing_project.path).resolve()
+
+        if requested_path == existing_path:
+            # Same name, same path - return 200 OK (idempotent)
+            response.status_code = 200
+            return ProjectStatusResponse(  # pyright: ignore [reportCallIssue]
+                message=f"Project '{project_data.name}' already exists",
+                status="success",
+                default=existing_project.is_default or False,
+                new_project=ProjectItem(
+                    name=existing_project.name,
+                    path=existing_project.path,
+                    is_default=existing_project.is_default or False,
+                ),
+            )
+        else:
+            # Same name, different path - this is an error
+            raise HTTPException(
+                status_code=400,
+                detail=f"Project '{project_data.name}' already exists with different path. Existing: {existing_project.path}, Requested: {project_data.path}",
+            )
+
     try:  # pragma: no cover
         # The service layer now handles cloud mode validation and path sanitization
         await project_service.add_project(
@@ -216,11 +267,15 @@ async def add_project(
 async def remove_project(
     project_service: ProjectServiceDep,
     name: str = Path(..., description="Name of the project to remove"),
+    delete_notes: bool = Query(
+        False, description="If True, delete project directory from filesystem"
+    ),
 ) -> ProjectStatusResponse:
     """Remove a project from configuration and database.
 
     Args:
         name: The name of the project to remove
+        delete_notes: If True, delete the project directory from the filesystem
 
     Returns:
         Response confirming the project was removed
@@ -232,7 +287,20 @@ async def remove_project(
                 status_code=404, detail=f"Project: '{name}' does not exist"
             )  # pragma: no cover
 
-        await project_service.remove_project(name)
+        # Check if trying to delete the default project
+        if name == project_service.default_project:
+            available_projects = await project_service.list_projects()
+            other_projects = [p.name for p in available_projects if p.name != name]
+            detail = f"Cannot delete default project '{name}'. "
+            if other_projects:
+                detail += (
+                    f"Set another project as default first. Available: {', '.join(other_projects)}"
+                )
+            else:
+                detail += "This is the only project in your configuration."
+            raise HTTPException(status_code=400, detail=detail)
+
+        await project_service.remove_project(name, delete_notes=delete_notes)
 
         return ProjectStatusResponse(
             message=f"Project '{name}' removed successfully",

src/basic_memory/api/routers/resource_router.py

@@ -151,6 +151,20 @@ async def write_resource(
     try:
         # Get content from request body
 
+        # Defensive type checking: ensure content is a string
+        # FastAPI should validate this, but if a dict somehow gets through
+        # (e.g., via JSON body parsing), we need to catch it here
+        if isinstance(content, dict):
+            logger.error(
+                f"Error writing resource {file_path}: "
+                f"content is a dict, expected string. Keys: {list(content.keys())}"
+            )
+            raise HTTPException(
+                status_code=400,
+                detail="content must be a string, not a dict. "
+                "Ensure request body is sent as raw string content, not JSON object.",
+            )
+
         # Ensure it's UTF-8 string content
         if isinstance(content, bytes):  # pragma: no cover
             content_str = content.decode("utf-8")

src/basic_memory/cli/auth.py

@@ -77,7 +77,7 @@ class CLIAuth:
         verification_uri = device_response["verification_uri"]
         verification_uri_complete = device_response.get("verification_uri_complete")
 
-        console.print("\n[bold blue]🔐 Authentication Required[/bold blue]")
+        console.print("\n[bold blue]Authentication Required[/bold blue]")
         console.print("\nTo authenticate, please visit:")
         console.print(f"[bold cyan]{verification_uri}[/bold cyan]")
         console.print(f"\nAnd enter this code: [bold yellow]{user_code}[/bold yellow]")
@@ -171,7 +171,7 @@ class CLIAuth:
         # Secure the token file
         os.chmod(self.token_file, 0o600)
 
-        console.print(f"[green]✓ Tokens saved to {self.token_file}[/green]")
+        console.print(f"[green]Tokens saved to {self.token_file}[/green]")
 
     def load_tokens(self) -> dict | None:
         """Load tokens from .bm-auth.json file."""
@@ -233,7 +233,7 @@ class CLIAuth:
             if new_tokens:
                 # Save new tokens (may include rotated refresh token)
                 self.save_tokens(new_tokens)
-                console.print("[green]✓ Token refreshed successfully[/green]")
+                console.print("[green]Token refreshed successfully[/green]")
                 return new_tokens["access_token"]
             else:
                 console.print("[yellow]Token refresh failed. Please run 'login' again.[/yellow]")
@@ -265,13 +265,13 @@ class CLIAuth:
         # Step 4: Save tokens
         self.save_tokens(tokens)
 
-        console.print("\n[green]✅ Successfully authenticated with Basic Memory Cloud![/green]")
+        console.print("\n[green]Successfully authenticated with Basic Memory Cloud![/green]")
         return True
 
     def logout(self) -> None:
         """Remove stored authentication tokens."""
         if self.token_file.exists():
             self.token_file.unlink()
-            console.print("[green]✓ Logged out successfully[/green]")
+            console.print("[green]Logged out successfully[/green]")
         else:
             console.print("[yellow]No stored authentication found[/yellow]")

src/basic_memory/cli/commands/__init__.py

@@ -1,11 +1,10 @@
 """CLI commands for basic-memory."""
 
-from . import status, sync, db, import_memory_json, mcp, import_claude_conversations
+from . import status, db, import_memory_json, mcp, import_claude_conversations
 from . import import_claude_projects, import_chatgpt, tool, project
 
 __all__ = [
     "status",
-    "sync",
     "db",
     "import_memory_json",
     "mcp",

src/basic_memory/cli/commands/cloud/__init__.py

@@ -2,4 +2,5 @@
 
 # Import all commands to register them with typer
 from basic_memory.cli.commands.cloud.core_commands import *  # noqa: F401,F403
-from basic_memory.cli.commands.cloud.api_client import get_authenticated_headers  # noqa: F401
+from basic_memory.cli.commands.cloud.api_client import get_authenticated_headers, get_cloud_config  # noqa: F401
+from basic_memory.cli.commands.cloud.upload_command import *  # noqa: F401,F403

src/basic_memory/cli/commands/cloud/bisync_commands.py

@@ -1,33 +1,11 @@
-"""Cloud bisync commands for Basic Memory CLI."""
+"""Cloud bisync utility functions for Basic Memory CLI."""
 
-import asyncio
-import subprocess
-import time
-from datetime import datetime
 from pathlib import Path
-from typing import Optional
 
-import typer
-from rich.console import Console
-from rich.table import Table
-
-from basic_memory.cli.commands.cloud.api_client import CloudAPIError, make_api_request
-from basic_memory.cli.commands.cloud.rclone_config import (
-    add_tenant_to_rclone_config,
-)
-from basic_memory.cli.commands.cloud.rclone_installer import RcloneInstallError, install_rclone
+from basic_memory.cli.commands.cloud.api_client import make_api_request
 from basic_memory.config import ConfigManager
-from basic_memory.ignore_utils import get_bmignore_path, create_default_bmignore
-from basic_memory.schemas.cloud import (
-    TenantMountInfo,
-    MountCredentials,
-    CloudProjectList,
-    CloudProjectCreateRequest,
-    CloudProjectCreateResponse,
-)
-from basic_memory.utils import generate_permalink
-
-console = Console()
+from basic_memory.ignore_utils import create_default_bmignore, get_bmignore_path
+from basic_memory.schemas.cloud import MountCredentials, TenantMountInfo
 
 
 class BisyncError(Exception):
@@ -36,52 +14,6 @@ class BisyncError(Exception):
     pass
 
 
-class RcloneBisyncProfile:
-    """Bisync profile with safety settings."""
-
-    def __init__(
-        self,
-        name: str,
-        conflict_resolve: str,
-        max_delete: int,
-        check_access: bool,
-        description: str,
-        extra_args: Optional[list[str]] = None,
-    ):
-        self.name = name
-        self.conflict_resolve = conflict_resolve
-        self.max_delete = max_delete
-        self.check_access = check_access
-        self.description = description
-        self.extra_args = extra_args or []
-
-
-# Bisync profiles based on SPEC-9 Phase 2.1
-BISYNC_PROFILES = {
-    "safe": RcloneBisyncProfile(
-        name="safe",
-        conflict_resolve="none",
-        max_delete=10,
-        check_access=False,
-        description="Safe mode with conflict preservation (keeps both versions)",
-    ),
-    "balanced": RcloneBisyncProfile(
-        name="balanced",
-        conflict_resolve="newer",
-        max_delete=25,
-        check_access=False,
-        description="Balanced mode - auto-resolve to newer file (recommended)",
-    ),
-    "fast": RcloneBisyncProfile(
-        name="fast",
-        conflict_resolve="newer",
-        max_delete=50,
-        check_access=False,
-        description="Fast mode for rapid iteration (skip verification)",
-    ),
-}
-
-
 async def get_mount_info() -> TenantMountInfo:
     """Get current tenant information from cloud API."""
     try:
@@ -110,128 +42,6 @@ async def generate_mount_credentials(tenant_id: str) -> MountCredentials:
         raise BisyncError(f"Failed to generate credentials: {e}") from e
 
 
-async def fetch_cloud_projects() -> CloudProjectList:
-    """Fetch list of projects from cloud API.
-
-    Returns:
-        CloudProjectList with projects from cloud
-    """
-    try:
-        config_manager = ConfigManager()
-        config = config_manager.config
-        host_url = config.cloud_host.rstrip("/")
-
-        response = await make_api_request(method="GET", url=f"{host_url}/proxy/projects/projects")
-
-        return CloudProjectList.model_validate(response.json())
-    except Exception as e:
-        raise BisyncError(f"Failed to fetch cloud projects: {e}") from e
-
-
-def scan_local_directories(sync_dir: Path) -> list[str]:
-    """Scan local sync directory for project folders.
-
-    Args:
-        sync_dir: Path to bisync directory
-
-    Returns:
-        List of directory names (project names)
-    """
-    if not sync_dir.exists():
-        return []
-
-    directories = []
-    for item in sync_dir.iterdir():
-        if item.is_dir() and not item.name.startswith("."):
-            directories.append(item.name)
-
-    return directories
-
-
-async def create_cloud_project(project_name: str) -> CloudProjectCreateResponse:
-    """Create a new project on cloud.
-
-    Args:
-        project_name: Name of project to create
-
-    Returns:
-        CloudProjectCreateResponse with project details from API
-    """
-    try:
-        config_manager = ConfigManager()
-        config = config_manager.config
-        host_url = config.cloud_host.rstrip("/")
-
-        # Use generate_permalink to ensure consistent naming
-        project_path = generate_permalink(project_name)
-
-        project_data = CloudProjectCreateRequest(
-            name=project_name,
-            path=project_path,
-            set_default=False,
-        )
-
-        response = await make_api_request(
-            method="POST",
-            url=f"{host_url}/proxy/projects/projects",
-            headers={"Content-Type": "application/json"},
-            json_data=project_data.model_dump(),
-        )
-
-        return CloudProjectCreateResponse.model_validate(response.json())
-    except Exception as e:
-        raise BisyncError(f"Failed to create cloud project '{project_name}': {e}") from e
-
-
-def get_bisync_state_path(tenant_id: str) -> Path:
-    """Get path to bisync state directory."""
-    return Path.home() / ".basic-memory" / "bisync-state" / tenant_id
-
-
-def get_bisync_directory() -> Path:
-    """Get bisync directory from config.
-
-    Returns:
-        Path to bisync directory (default: ~/basic-memory-cloud-sync)
-    """
-    config_manager = ConfigManager()
-    config = config_manager.config
-
-    sync_dir = config.bisync_config.get("sync_dir", str(Path.home() / "basic-memory-cloud-sync"))
-    return Path(sync_dir).expanduser().resolve()
-
-
-def validate_bisync_directory(bisync_dir: Path) -> None:
-    """Validate bisync directory doesn't conflict with mount.
-
-    Raises:
-        BisyncError: If bisync directory conflicts with mount directory
-    """
-    # Get fixed mount directory
-    mount_dir = (Path.home() / "basic-memory-cloud").resolve()
-
-    # Check if bisync dir is the same as mount dir
-    if bisync_dir == mount_dir:
-        raise BisyncError(
-            f"Cannot use {bisync_dir} for bisync - it's the mount directory!\n"
-            f"Mount and bisync must use different directories.\n\n"
-            f"Options:\n"
-            f"  1. Use default: ~/basic-memory-cloud-sync/\n"
-            f"  2. Specify different directory: --dir ~/my-sync-folder"
-        )
-
-    # Check if mount is active at this location
-    result = subprocess.run(["mount"], capture_output=True, text=True)
-    if str(bisync_dir) in result.stdout and "rclone" in result.stdout:
-        raise BisyncError(
-            f"{bisync_dir} is currently mounted via 'bm cloud mount'\n"
-            f"Cannot use mounted directory for bisync.\n\n"
-            f"Either:\n"
-            f"  1. Unmount first: bm cloud unmount\n"
-            f"  2. Use different directory for bisync"
-        )
-
-
 def convert_bmignore_to_rclone_filters() -> Path:
     """Convert .bmignore patterns to rclone filter format.
 
@@ -298,521 +108,3 @@ def get_bisync_filter_path() -> Path:
         Path to rclone filter file
     """
     return convert_bmignore_to_rclone_filters()
-
-
-def bisync_state_exists(tenant_id: str) -> bool:
-    """Check if bisync state exists (has been initialized)."""
-    state_path = get_bisync_state_path(tenant_id)
-    return state_path.exists() and any(state_path.iterdir())
-
-
-def build_bisync_command(
-    tenant_id: str,
-    bucket_name: str,
-    local_path: Path,
-    profile: RcloneBisyncProfile,
-    dry_run: bool = False,
-    resync: bool = False,
-    verbose: bool = False,
-) -> list[str]:
-    """Build rclone bisync command with profile settings."""
-
-    # Sync with the entire bucket root (all projects)
-    rclone_remote = f"basic-memory-{tenant_id}:{bucket_name}"
-    filter_path = get_bisync_filter_path()
-    state_path = get_bisync_state_path(tenant_id)
-
-    # Ensure state directory exists
-    state_path.mkdir(parents=True, exist_ok=True)
-
-    cmd = [
-        "rclone",
-        "bisync",
-        str(local_path),
-        rclone_remote,
-        "--create-empty-src-dirs",
-        "--resilient",
-        f"--conflict-resolve={profile.conflict_resolve}",
-        f"--max-delete={profile.max_delete}",
-        "--filters-file",
-        str(filter_path),
-        "--workdir",
-        str(state_path),
-    ]
-
-    # Add verbosity flags
-    if verbose:
-        cmd.append("--verbose")  # Full details with file-by-file output
-    else:
-        # Show progress bar during transfers
-        cmd.append("--progress")
-
-    if profile.check_access:
-        cmd.append("--check-access")
-
-    if dry_run:
-        cmd.append("--dry-run")
-
-    if resync:
-        cmd.append("--resync")
-
-    cmd.extend(profile.extra_args)
-
-    return cmd
-
-
-def setup_cloud_bisync(sync_dir: Optional[str] = None) -> None:
-    """Set up cloud bisync with rclone installation and configuration.
-
-    Args:
-        sync_dir: Optional custom sync directory path. If not provided, uses config default.
-    """
-    console.print("[bold blue]Basic Memory Cloud Bisync Setup[/bold blue]")
-    console.print("Setting up bidirectional sync to your cloud tenant...\n")
-
-    try:
-        # Step 1: Install rclone
-        console.print("[blue]Step 1: Installing rclone...[/blue]")
-        install_rclone()
-
-        # Step 2: Get mount info (for tenant_id, bucket)
-        console.print("\n[blue]Step 2: Getting tenant information...[/blue]")
-        tenant_info = asyncio.run(get_mount_info())
-
-        tenant_id = tenant_info.tenant_id
-        bucket_name = tenant_info.bucket_name
-
-        console.print(f"[green]✓ Found tenant: {tenant_id}[/green]")
-        console.print(f"[green]✓ Bucket: {bucket_name}[/green]")
-
-        # Step 3: Generate credentials
-        console.print("\n[blue]Step 3: Generating sync credentials...[/blue]")
-        creds = asyncio.run(generate_mount_credentials(tenant_id))
-
-        access_key = creds.access_key
-        secret_key = creds.secret_key
-
-        console.print("[green]✓ Generated secure credentials[/green]")
-
-        # Step 4: Configure rclone
-        console.print("\n[blue]Step 4: Configuring rclone...[/blue]")
-        add_tenant_to_rclone_config(
-            tenant_id=tenant_id,
-            bucket_name=bucket_name,
-            access_key=access_key,
-            secret_key=secret_key,
-        )
-
-        # Step 5: Configure and create local directory
-        console.print("\n[blue]Step 5: Configuring sync directory...[/blue]")
-
-        # If custom sync_dir provided, save to config
-        if sync_dir:
-            config_manager = ConfigManager()
-            config = config_manager.load_config()
-            config.bisync_config["sync_dir"] = sync_dir
-            config_manager.save_config(config)
-            console.print("[green]✓ Saved custom sync directory to config[/green]")
-
-        # Get bisync directory (from config or default)
-        local_path = get_bisync_directory()
-
-        # Validate bisync directory
-        validate_bisync_directory(local_path)
-
-        # Create directory
-        local_path.mkdir(parents=True, exist_ok=True)
-        console.print(f"[green]✓ Created sync directory: {local_path}[/green]")
-
-        # Step 6: Perform initial resync
-        console.print("\n[blue]Step 6: Performing initial sync...[/blue]")
-        console.print("[yellow]This will establish the baseline for bidirectional sync.[/yellow]")
-
-        run_bisync(
-            tenant_id=tenant_id,
-            bucket_name=bucket_name,
-            local_path=local_path,
-            profile_name="balanced",
-            resync=True,
-        )
-
-        console.print("\n[bold green]✓ Bisync setup completed successfully![/bold green]")
-        console.print("\nYour local files will now sync bidirectionally with the cloud!")
-        console.print(f"\nLocal directory: {local_path}")
-        console.print("\nUseful commands:")
-        console.print("  bm sync                      # Run sync (recommended)")
-        console.print("  bm sync --watch              # Start watch mode")
-        console.print("  bm cloud status              # Check sync status")
-        console.print("  bm cloud check               # Verify file integrity")
-        console.print("  bm cloud bisync --dry-run    # Preview changes (advanced)")
-
-    except (RcloneInstallError, BisyncError, CloudAPIError) as e:
-        console.print(f"\n[red]Setup failed: {e}[/red]")
-        raise typer.Exit(1)
-    except Exception as e:
-        console.print(f"\n[red]Unexpected error during setup: {e}[/red]")
-        raise typer.Exit(1)
-
-
-def run_bisync(
-    tenant_id: Optional[str] = None,
-    bucket_name: Optional[str] = None,
-    local_path: Optional[Path] = None,
-    profile_name: str = "balanced",
-    dry_run: bool = False,
-    resync: bool = False,
-    verbose: bool = False,
-) -> bool:
-    """Run rclone bisync with specified profile."""
-
-    try:
-        # Get tenant info if not provided
-        if not tenant_id or not bucket_name:
-            tenant_info = asyncio.run(get_mount_info())
-            tenant_id = tenant_info.tenant_id
-            bucket_name = tenant_info.bucket_name
-
-        # Set default local path if not provided
-        if not local_path:
-            local_path = get_bisync_directory()
-
-        # Validate bisync directory
-        validate_bisync_directory(local_path)
-
-        # Check if local path exists
-        if not local_path.exists():
-            raise BisyncError(
-                f"Local directory {local_path} does not exist. Run 'basic-memory cloud bisync-setup' first."
-            )
-
-        # Get bisync profile
-        if profile_name not in BISYNC_PROFILES:
-            raise BisyncError(
-                f"Unknown profile: {profile_name}. Available: {list(BISYNC_PROFILES.keys())}"
-            )
-
-        profile = BISYNC_PROFILES[profile_name]
-
-        # Auto-register projects before sync (unless dry-run or resync)
-        if not dry_run and not resync:
-            try:
-                console.print("[dim]Checking for new projects...[/dim]")
-
-                # Fetch cloud projects and extract directory names from paths
-                cloud_data = asyncio.run(fetch_cloud_projects())
-                cloud_projects = cloud_data.projects
-
-                # Extract directory names from cloud project paths
-                # Compare directory names, not project names
-                # Cloud path /app/data/basic-memory -> directory name "basic-memory"
-                cloud_dir_names = set()
-                for p in cloud_projects:
-                    path = p.path
-                    # Strip /app/data/ prefix if present (cloud mode)
-                    if path.startswith("/app/data/"):
-                        path = path[len("/app/data/") :]
-                    # Get the last segment (directory name)
-                    dir_name = Path(path).name
-                    cloud_dir_names.add(dir_name)
-
-                # Scan local directories
-                local_dirs = scan_local_directories(local_path)
-
-                # Create missing cloud projects
-                new_projects = []
-                for dir_name in local_dirs:
-                    if dir_name not in cloud_dir_names:
-                        new_projects.append(dir_name)
-
-                if new_projects:
-                    console.print(
-                        f"[blue]Found {len(new_projects)} new local project(s), creating on cloud...[/blue]"
-                    )
-                    for project_name in new_projects:
-                        try:
-                            asyncio.run(create_cloud_project(project_name))
-                            console.print(f"[green]  ✓ Created project: {project_name}[/green]")
-                        except BisyncError as e:
-                            console.print(
-                                f"[yellow]  ⚠ Could not create {project_name}: {e}[/yellow]"
-                            )
-                else:
-                    console.print("[dim]All local projects already registered on cloud[/dim]")
-
-            except Exception as e:
-                console.print(f"[yellow]Warning: Project auto-registration failed: {e}[/yellow]")
-                console.print("[yellow]Continuing with sync anyway...[/yellow]")
-
-        # Check if first run and require resync
-        if not resync and not bisync_state_exists(tenant_id) and not dry_run:
-            raise BisyncError(
-                "First bisync requires --resync to establish baseline. "
-                "Run: basic-memory cloud bisync --resync"
-            )
-
-        # Build and execute bisync command
-        bisync_cmd = build_bisync_command(
-            tenant_id,
-            bucket_name,
-            local_path,
-            profile,
-            dry_run=dry_run,
-            resync=resync,
-            verbose=verbose,
-        )
-
-        if dry_run:
-            console.print("[yellow]DRY RUN MODE - No changes will be made[/yellow]")
-
-        console.print(
-            f"[blue]Running bisync with profile '{profile_name}' ({profile.description})...[/blue]"
-        )
-        console.print(f"[dim]Command: {' '.join(bisync_cmd)}[/dim]")
-        console.print()  # Blank line before output
-
-        # Stream output in real-time so user sees progress
-        result = subprocess.run(bisync_cmd, text=True)
-
-        if result.returncode != 0:
-            raise BisyncError(f"Bisync command failed with code {result.returncode}")
-
-        console.print()  # Blank line after output
-
-        if dry_run:
-            console.print("[green]✓ Dry run completed successfully[/green]")
-        elif resync:
-            console.print("[green]✓ Initial sync baseline established[/green]")
-        else:
-            console.print("[green]✓ Sync completed successfully[/green]")
-
-        # Notify container to refresh cache (if not dry run)
-        if not dry_run:
-            try:
-                asyncio.run(notify_container_sync(tenant_id))
-            except Exception as e:
-                console.print(f"[yellow]Warning: Could not notify container: {e}[/yellow]")
-
-        return True
-
-    except BisyncError:
-        raise
-    except Exception as e:
-        raise BisyncError(f"Unexpected error during bisync: {e}") from e
-
-
-async def notify_container_sync(tenant_id: str) -> None:
-    """Sync all projects after bisync completes."""
-    try:
-        from basic_memory.cli.commands.command_utils import run_sync
-
-        # Fetch all projects and sync each one
-        cloud_data = await fetch_cloud_projects()
-        projects = cloud_data.projects
-
-        if not projects:
-            console.print("[dim]No projects to sync[/dim]")
-            return
-
-        console.print(f"[blue]Notifying cloud to index {len(projects)} project(s)...[/blue]")
-
-        for project in projects:
-            project_name = project.name
-            if project_name:
-                try:
-                    await run_sync(project=project_name)
-                except Exception as e:
-                    # Non-critical, log and continue
-                    console.print(f"[yellow]  ⚠ Sync failed for {project_name}: {e}[/yellow]")
-
-        console.print("[dim]Note: Cloud indexing has started and may take a few moments[/dim]")
-
-    except Exception as e:
-        # Non-critical, don't fail the bisync
-        console.print(f"[yellow]Warning: Post-sync failed: {e}[/yellow]")
-
-
-def run_bisync_watch(
-    tenant_id: Optional[str] = None,
-    bucket_name: Optional[str] = None,
-    local_path: Optional[Path] = None,
-    profile_name: str = "balanced",
-    interval_seconds: int = 60,
-) -> None:
-    """Run bisync in watch mode with periodic syncs."""
-
-    console.print("[bold blue]Starting bisync watch mode[/bold blue]")
-    console.print(f"Sync interval: {interval_seconds} seconds")
-    console.print("Press Ctrl+C to stop\n")
-
-    try:
-        while True:
-            try:
-                start_time = time.time()
-
-                run_bisync(
-                    tenant_id=tenant_id,
-                    bucket_name=bucket_name,
-                    local_path=local_path,
-                    profile_name=profile_name,
-                )
-
-                elapsed = time.time() - start_time
-                console.print(f"[dim]Sync completed in {elapsed:.1f}s[/dim]")
-
-                # Wait for next interval
-                time.sleep(interval_seconds)
-
-            except BisyncError as e:
-                console.print(f"[red]Sync error: {e}[/red]")
-                console.print(f"[yellow]Retrying in {interval_seconds} seconds...[/yellow]")
-                time.sleep(interval_seconds)
-
-    except KeyboardInterrupt:
-        console.print("\n[yellow]Watch mode stopped[/yellow]")
-
-
-def show_bisync_status() -> None:
-    """Show current bisync status and configuration."""
-
-    try:
-        # Get tenant info
-        tenant_info = asyncio.run(get_mount_info())
-        tenant_id = tenant_info.tenant_id
-
-        local_path = get_bisync_directory()
-        state_path = get_bisync_state_path(tenant_id)
-
-        # Create status table
-        table = Table(title="Cloud Bisync Status", show_header=True, header_style="bold blue")
-        table.add_column("Property", style="green", min_width=20)
-        table.add_column("Value", style="dim", min_width=30)
-
-        # Check initialization status
-        is_initialized = bisync_state_exists(tenant_id)
-        init_status = (
-            "[green]✓ Initialized[/green]" if is_initialized else "[red]✗ Not initialized[/red]"
-        )
-
-        table.add_row("Tenant ID", tenant_id)
-        table.add_row("Local Directory", str(local_path))
-        table.add_row("Status", init_status)
-        table.add_row("State Directory", str(state_path))
-
-        # Check for last sync info
-        if is_initialized:
-            # Look for most recent state file
-            state_files = list(state_path.glob("*.lst"))
-            if state_files:
-                latest = max(state_files, key=lambda p: p.stat().st_mtime)
-                last_sync = datetime.fromtimestamp(latest.stat().st_mtime)
-                table.add_row("Last Sync", last_sync.strftime("%Y-%m-%d %H:%M:%S"))
-
-        console.print(table)
-
-        # Show bisync profiles
-        console.print("\n[bold]Available bisync profiles:[/bold]")
-        for name, profile in BISYNC_PROFILES.items():
-            console.print(f"  {name}: {profile.description}")
-            console.print(f"    - Conflict resolution: {profile.conflict_resolve}")
-            console.print(f"    - Max delete: {profile.max_delete} files")
-
-        console.print("\n[dim]To use a profile: bm cloud bisync --profile <name>[/dim]")
-
-        # Show setup instructions if not initialized
-        if not is_initialized:
-            console.print("\n[yellow]To initialize bisync, run:[/yellow]")
-            console.print("  bm cloud setup")
-            console.print("  or")
-            console.print("  bm cloud bisync --resync")
-
-    except Exception as e:
-        console.print(f"[red]Error getting bisync status: {e}[/red]")
-        raise typer.Exit(1)
-
-
-def run_check(
-    tenant_id: Optional[str] = None,
-    bucket_name: Optional[str] = None,
-    local_path: Optional[Path] = None,
-    one_way: bool = False,
-) -> bool:
-    """Check file integrity between local and cloud using rclone check.
-
-    Args:
-        tenant_id: Cloud tenant ID (auto-detected if not provided)
-        bucket_name: S3 bucket name (auto-detected if not provided)
-        local_path: Local bisync directory (uses config default if not provided)
-        one_way: If True, only check for missing files on destination (faster)
-
-    Returns:
-        True if check passed (files match), False if differences found
-    """
-    try:
-        # Check if rclone is installed
-        from basic_memory.cli.commands.cloud.rclone_installer import is_rclone_installed
-
-        if not is_rclone_installed():
-            raise BisyncError(
-                "rclone is not installed. Run 'bm cloud bisync-setup' first to set up cloud sync."
-            )
-
-        # Get tenant info if not provided
-        if not tenant_id or not bucket_name:
-            tenant_info = asyncio.run(get_mount_info())
-            tenant_id = tenant_id or tenant_info.tenant_id
-            bucket_name = bucket_name or tenant_info.bucket_name
-
-        # Get local path from config
-        if not local_path:
-            local_path = get_bisync_directory()
-
-        # Check if bisync is initialized
-        if not bisync_state_exists(tenant_id):
-            raise BisyncError(
-                "Bisync not initialized. Run 'bm cloud bisync --resync' to establish baseline."
-            )
-
-        # Build rclone check command
-        rclone_remote = f"basic-memory-{tenant_id}:{bucket_name}"
-        filter_path = get_bisync_filter_path()
-
-        cmd = [
-            "rclone",
-            "check",
-            str(local_path),
-            rclone_remote,
-            "--filter-from",
-            str(filter_path),
-        ]
-
-        if one_way:
-            cmd.append("--one-way")
-
-        console.print("[bold blue]Checking file integrity between local and cloud[/bold blue]")
-        console.print(f"[dim]Local:  {local_path}[/dim]")
-        console.print(f"[dim]Remote: {rclone_remote}[/dim]")
-        console.print(f"[dim]Command: {' '.join(cmd)}[/dim]")
-        console.print()
-
-        # Run check command
-        result = subprocess.run(cmd, capture_output=True, text=True)
-
-        # rclone check returns:
-        # 0 = success (all files match)
-        # non-zero = differences found or error
-        if result.returncode == 0:
-            console.print("[green]✓ All files match between local and cloud[/green]")
-            return True
-        else:
-            console.print("[yellow]⚠ Differences found:[/yellow]")
-            if result.stderr:
-                console.print(result.stderr)
-            if result.stdout:
-                console.print(result.stdout)
-            console.print("\n[dim]To sync differences, run: bm sync[/dim]")
-            return False
-
-    except BisyncError:
-        raise
-    except Exception as e:
-        raise BisyncError(f"Check failed: {e}") from e

src/basic_memory/cli/commands/cloud/cloud_utils.py

@@ -0,0 +1,101 @@
+"""Shared utilities for cloud operations."""
+
+from basic_memory.cli.commands.cloud.api_client import make_api_request
+from basic_memory.config import ConfigManager
+from basic_memory.schemas.cloud import (
+    CloudProjectList,
+    CloudProjectCreateRequest,
+    CloudProjectCreateResponse,
+)
+from basic_memory.utils import generate_permalink
+
+
+class CloudUtilsError(Exception):
+    """Exception raised for cloud utility errors."""
+
+    pass
+
+
+async def fetch_cloud_projects() -> CloudProjectList:
+    """Fetch list of projects from cloud API.
+
+    Returns:
+        CloudProjectList with projects from cloud
+    """
+    try:
+        config_manager = ConfigManager()
+        config = config_manager.config
+        host_url = config.cloud_host.rstrip("/")
+
+        response = await make_api_request(method="GET", url=f"{host_url}/proxy/projects/projects")
+
+        return CloudProjectList.model_validate(response.json())
+    except Exception as e:
+        raise CloudUtilsError(f"Failed to fetch cloud projects: {e}") from e
+
+
+async def create_cloud_project(project_name: str) -> CloudProjectCreateResponse:
+    """Create a new project on cloud.
+
+    Args:
+        project_name: Name of project to create
+
+    Returns:
+        CloudProjectCreateResponse with project details from API
+    """
+    try:
+        config_manager = ConfigManager()
+        config = config_manager.config
+        host_url = config.cloud_host.rstrip("/")
+
+        # Use generate_permalink to ensure consistent naming
+        project_path = generate_permalink(project_name)
+
+        project_data = CloudProjectCreateRequest(
+            name=project_name,
+            path=project_path,
+            set_default=False,
+        )
+
+        response = await make_api_request(
+            method="POST",
+            url=f"{host_url}/proxy/projects/projects",
+            headers={"Content-Type": "application/json"},
+            json_data=project_data.model_dump(),
+        )
+
+        return CloudProjectCreateResponse.model_validate(response.json())
+    except Exception as e:
+        raise CloudUtilsError(f"Failed to create cloud project '{project_name}': {e}") from e
+
+
+async def sync_project(project_name: str, force_full: bool = False) -> None:
+    """Trigger sync for a specific project on cloud.
+
+    Args:
+        project_name: Name of project to sync
+        force_full: If True, force a full scan bypassing watermark optimization
+    """
+    try:
+        from basic_memory.cli.commands.command_utils import run_sync
+
+        await run_sync(project=project_name, force_full=force_full)
+    except Exception as e:
+        raise CloudUtilsError(f"Failed to sync project '{project_name}': {e}") from e
+
+
+async def project_exists(project_name: str) -> bool:
+    """Check if a project exists on cloud.
+
+    Args:
+        project_name: Name of project to check
+
+    Returns:
+        True if project exists, False otherwise
+    """
+    try:
+        projects = await fetch_cloud_projects()
+        project_names = {p.name for p in projects.projects}
+        return project_name in project_names
+    except Exception:
+        return False

src/basic_memory/cli/commands/cloud/core_commands.py

@@ -1,7 +1,6 @@
 """Core cloud commands for Basic Memory CLI."""
 
 import asyncio
-from typing import Optional
 
 import typer
 from rich.console import Console
@@ -15,21 +14,16 @@ from basic_memory.cli.commands.cloud.api_client import (
     get_cloud_config,
     make_api_request,
 )
-from basic_memory.cli.commands.cloud.mount_commands import (
-    mount_cloud_files,
-    setup_cloud_mount,
-    show_mount_status,
-    unmount_cloud_files,
-)
 from basic_memory.cli.commands.cloud.bisync_commands import (
-    run_bisync,
-    run_bisync_watch,
-    run_check,
-    setup_cloud_bisync,
-    show_bisync_status,
+    BisyncError,
+    generate_mount_credentials,
+    get_mount_info,
+)
+from basic_memory.cli.commands.cloud.rclone_config import configure_rclone_remote
+from basic_memory.cli.commands.cloud.rclone_installer import (
+    RcloneInstallError,
+    install_rclone,
 )
-from basic_memory.cli.commands.cloud.rclone_config import MOUNT_PROFILES
-from basic_memory.cli.commands.cloud.bisync_commands import BISYNC_PROFILES
 
 console = Console()
 
@@ -58,11 +52,11 @@ def login():
             config.cloud_mode = True
             config_manager.save_config(config)
 
-            console.print("[green]✓ Cloud mode enabled[/green]")
+            console.print("[green]Cloud mode enabled[/green]")
             console.print(f"[dim]All CLI commands now work against {host_url}[/dim]")
 
         except SubscriptionRequiredError as e:
-            console.print("\n[red]✗ Subscription Required[/red]\n")
+            console.print("\n[red]Subscription Required[/red]\n")
             console.print(f"[yellow]{e.args[0]}[/yellow]\n")
             console.print(f"Subscribe at: [blue underline]{e.subscribe_url}[/blue underline]\n")
             console.print(
@@ -83,23 +77,13 @@ def logout():
     config.cloud_mode = False
     config_manager.save_config(config)
 
-    console.print("[green]✓ Cloud mode disabled[/green]")
+    console.print("[green]Cloud mode disabled[/green]")
     console.print("[dim]All CLI commands now work locally[/dim]")
 
 
 @cloud_app.command("status")
-def status(
-    bisync: bool = typer.Option(
-        True,
-        "--bisync/--mount",
-        help="Show bisync status (default) or mount status",
-    ),
-) -> None:
-    """Check cloud mode status and cloud instance health.
-
-    Shows cloud mode status, instance health, and sync/mount status.
-    Use --bisync (default) to show bisync status or --mount for mount status.
-    """
+def status() -> None:
+    """Check cloud mode status and cloud instance health."""
     # Check cloud mode
     config_manager = ConfigManager()
     config = config_manager.load_config()
@@ -142,12 +126,7 @@ def status(
         if "timestamp" in health_data:
             console.print(f"  Timestamp: {health_data['timestamp']}")
 
-        # Show sync/mount status based on flag
-        console.print()
-        if bisync:
-            show_bisync_status()
-        else:
-            show_mount_status()
+        console.print("\n[dim]To sync projects, use: bm project bisync --name <project>[/dim]")
 
     except CloudAPIError as e:
         console.print(f"[red]Error checking cloud health: {e}[/red]")
@@ -157,132 +136,60 @@ def status(
         raise typer.Exit(1)
 
 
-# Mount commands
-
-
 @cloud_app.command("setup")
-def setup(
-    bisync: bool = typer.Option(
-        True,
-        "--bisync/--mount",
-        help="Use bidirectional sync (recommended) or mount as network drive",
-    ),
-    sync_dir: Optional[str] = typer.Option(
-        None,
-        "--dir",
-        help="Custom sync directory for bisync (default: ~/basic-memory-cloud-sync)",
-    ),
-) -> None:
-    """Set up cloud file access with automatic rclone installation and configuration.
+def setup() -> None:
+    """Set up cloud sync by installing rclone and configuring credentials.
 
-    Default: Sets up bidirectional sync (recommended).\n
-    Use --mount: Sets up mount as network drive (alternative workflow).\n
-
-    Examples:\n
-      bm cloud setup              # Setup bisync (default)\n
-      bm cloud setup --mount      # Setup mount instead\n
-      bm cloud setup --dir ~/sync # Custom bisync directory\n
+    SPEC-20: Simplified to project-scoped workflow.
+    After setup, use project commands for syncing:
+      bm project add <name> <path> --local-path ~/projects/<name>
+      bm project bisync --name <name> --resync  # First time
+      bm project bisync --name <name>            # Subsequent syncs
     """
-    if bisync:
-        setup_cloud_bisync(sync_dir=sync_dir)
-    else:
-        setup_cloud_mount()
+    console.print("[bold blue]Basic Memory Cloud Setup[/bold blue]")
+    console.print("Setting up cloud sync with rclone...\n")
 
-
-@cloud_app.command("mount")
-def mount(
-    profile: str = typer.Option(
-        "balanced", help=f"Mount profile: {', '.join(MOUNT_PROFILES.keys())}"
-    ),
-    path: Optional[str] = typer.Option(
-        None, help="Custom mount path (default: ~/basic-memory-{tenant-id})"
-    ),
-) -> None:
-    """Mount cloud files locally for editing."""
     try:
-        mount_cloud_files(profile_name=profile)
-    except Exception as e:
-        console.print(f"[red]Mount failed: {e}[/red]")
+        # Step 1: Install rclone
+        console.print("[blue]Step 1: Installing rclone...[/blue]")
+        install_rclone()
+
+        # Step 2: Get tenant info
+        console.print("\n[blue]Step 2: Getting tenant information...[/blue]")
+        tenant_info = asyncio.run(get_mount_info())
+        console.print(f"[green]Found tenant: {tenant_info.tenant_id}[/green]")
+
+        # Step 3: Generate credentials
+        console.print("\n[blue]Step 3: Generating sync credentials...[/blue]")
+        creds = asyncio.run(generate_mount_credentials(tenant_info.tenant_id))
+        console.print("[green]Generated secure credentials[/green]")
+
+        # Step 4: Configure rclone remote
+        console.print("\n[blue]Step 4: Configuring rclone remote...[/blue]")
+        configure_rclone_remote(
+            access_key=creds.access_key,
+            secret_key=creds.secret_key,
+        )
+
+        console.print("\n[bold green]Cloud setup completed successfully![/bold green]")
+        console.print("\n[bold]Next steps:[/bold]")
+        console.print("1. Add a project with local sync path:")
+        console.print("   bm project add research --local-path ~/Documents/research")
+        console.print("\n   Or configure sync for an existing project:")
+        console.print("   bm project sync-setup research ~/Documents/research")
+        console.print("\n2. Preview the initial sync (recommended):")
+        console.print("   bm project bisync --name research --resync --dry-run")
+        console.print("\n3. If all looks good, run the actual sync:")
+        console.print("   bm project bisync --name research --resync")
+        console.print("\n4. Subsequent syncs (no --resync needed):")
+        console.print("   bm project bisync --name research")
+        console.print(
+            "\n[dim]Tip: Always use --dry-run first to preview changes before syncing[/dim]"
+        )
+
+    except (RcloneInstallError, BisyncError, CloudAPIError) as e:
+        console.print(f"\n[red]Setup failed: {e}[/red]")
         raise typer.Exit(1)
-
-
-@cloud_app.command("unmount")
-def unmount() -> None:
-    """Unmount cloud files."""
-    try:
-        unmount_cloud_files()
     except Exception as e:
-        console.print(f"[red]Unmount failed: {e}[/red]")
-        raise typer.Exit(1)
-
-
-# Bisync commands
-
-
-@cloud_app.command("bisync")
-def bisync(
-    profile: str = typer.Option(
-        "balanced", help=f"Bisync profile: {', '.join(BISYNC_PROFILES.keys())}"
-    ),
-    dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
-    resync: bool = typer.Option(False, "--resync", help="Force resync to establish new baseline"),
-    watch: bool = typer.Option(False, "--watch", help="Run continuous sync in watch mode"),
-    interval: int = typer.Option(60, "--interval", help="Sync interval in seconds for watch mode"),
-    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed sync output"),
-) -> None:
-    """Run bidirectional sync between local files and cloud storage.
-
-    Examples:
-      basic-memory cloud bisync                    # Manual sync with balanced profile
-      basic-memory cloud bisync --dry-run          # Preview what would be synced
-      basic-memory cloud bisync --resync           # Establish new baseline
-      basic-memory cloud bisync --watch            # Continuous sync every 60s
-      basic-memory cloud bisync --watch --interval 30  # Continuous sync every 30s
-      basic-memory cloud bisync --profile safe     # Use safe profile (keep conflicts)
-      basic-memory cloud bisync --verbose          # Show detailed file sync output
-    """
-    try:
-        if watch:
-            run_bisync_watch(profile_name=profile, interval_seconds=interval)
-        else:
-            run_bisync(profile_name=profile, dry_run=dry_run, resync=resync, verbose=verbose)
-    except Exception as e:
-        console.print(f"[red]Bisync failed: {e}[/red]")
-        raise typer.Exit(1)
-
-
-@cloud_app.command("bisync-status")
-def bisync_status() -> None:
-    """Show current bisync status and configuration.
-
-    DEPRECATED: Use 'bm cloud status' instead (bisync is now the default).
-    """
-    console.print(
-        "[yellow]Note: 'bisync-status' is deprecated. Use 'bm cloud status' instead.[/yellow]"
-    )
-    console.print("[dim]Showing bisync status...[/dim]\n")
-    show_bisync_status()
-
-
-@cloud_app.command("check")
-def check(
-    one_way: bool = typer.Option(
-        False,
-        "--one-way",
-        help="Only check for missing files on destination (faster)",
-    ),
-) -> None:
-    """Check file integrity between local and cloud storage using rclone check.
-
-    Verifies that files match between your local bisync directory and cloud storage
-    without transferring any data. This is useful for validating sync integrity.
-
-    Examples:
-      bm cloud check              # Full integrity check
-      bm cloud check --one-way    # Faster check (missing files only)
-    """
-    try:
-        run_check(one_way=one_way)
-    except Exception as e:
-        console.print(f"[red]Check failed: {e}[/red]")
+        console.print(f"\n[red]Unexpected error during setup: {e}[/red]")
         raise typer.Exit(1)

src/basic_memory/cli/commands/cloud/mount_commands.py

@@ -1,295 +0,0 @@
-"""Cloud mount commands for Basic Memory CLI."""
-
-import asyncio
-import subprocess
-import time
-from pathlib import Path
-from typing import Optional
-
-import typer
-from rich.console import Console
-from rich.table import Table
-
-from basic_memory.cli.commands.cloud.api_client import CloudAPIError, make_api_request
-from basic_memory.cli.commands.cloud.rclone_config import (
-    MOUNT_PROFILES,
-    add_tenant_to_rclone_config,
-    build_mount_command,
-    cleanup_orphaned_rclone_processes,
-    get_default_mount_path,
-    get_rclone_processes,
-    is_path_mounted,
-    unmount_path,
-)
-from basic_memory.cli.commands.cloud.rclone_installer import RcloneInstallError, install_rclone
-from basic_memory.config import ConfigManager
-
-console = Console()
-
-
-class MountError(Exception):
-    """Exception raised for mount-related errors."""
-
-    pass
-
-
-async def get_tenant_info() -> dict:
-    """Get current tenant information from cloud API."""
-    try:
-        config_manager = ConfigManager()
-        config = config_manager.config
-        host_url = config.cloud_host.rstrip("/")
-
-        response = await make_api_request(method="GET", url=f"{host_url}/tenant/mount/info")
-
-        return response.json()
-    except Exception as e:
-        raise MountError(f"Failed to get tenant info: {e}") from e
-
-
-async def generate_mount_credentials(tenant_id: str) -> dict:
-    """Generate scoped credentials for mounting."""
-    try:
-        config_manager = ConfigManager()
-        config = config_manager.config
-        host_url = config.cloud_host.rstrip("/")
-
-        response = await make_api_request(method="POST", url=f"{host_url}/tenant/mount/credentials")
-
-        return response.json()
-    except Exception as e:
-        raise MountError(f"Failed to generate mount credentials: {e}") from e
-
-
-def setup_cloud_mount() -> None:
-    """Set up cloud mount with rclone installation and configuration."""
-    console.print("[bold blue]Basic Memory Cloud Setup[/bold blue]")
-    console.print("Setting up local file access to your cloud tenant...\n")
-
-    try:
-        # Step 1: Install rclone
-        console.print("[blue]Step 1: Installing rclone...[/blue]")
-        install_rclone()
-
-        # Step 2: Get tenant info
-        console.print("\n[blue]Step 2: Getting tenant information...[/blue]")
-        tenant_info = asyncio.run(get_tenant_info())
-
-        tenant_id = tenant_info.get("tenant_id")
-        bucket_name = tenant_info.get("bucket_name")
-
-        if not tenant_id or not bucket_name:
-            raise MountError("Invalid tenant information received from cloud API")
-
-        console.print(f"[green]✓ Found tenant: {tenant_id}[/green]")
-        console.print(f"[green]✓ Bucket: {bucket_name}[/green]")
-
-        # Step 3: Generate mount credentials
-        console.print("\n[blue]Step 3: Generating mount credentials...[/blue]")
-        creds = asyncio.run(generate_mount_credentials(tenant_id))
-
-        access_key = creds.get("access_key")
-        secret_key = creds.get("secret_key")
-
-        if not access_key or not secret_key:
-            raise MountError("Failed to generate mount credentials")
-
-        console.print("[green]✓ Generated secure credentials[/green]")
-
-        # Step 4: Configure rclone
-        console.print("\n[blue]Step 4: Configuring rclone...[/blue]")
-        add_tenant_to_rclone_config(
-            tenant_id=tenant_id,
-            bucket_name=bucket_name,
-            access_key=access_key,
-            secret_key=secret_key,
-        )
-
-        # Step 5: Perform initial mount
-        console.print("\n[blue]Step 5: Mounting cloud files...[/blue]")
-        mount_path = get_default_mount_path()
-        MOUNT_PROFILES["balanced"]
-
-        mount_cloud_files(
-            tenant_id=tenant_id,
-            bucket_name=bucket_name,
-            mount_path=mount_path,
-            profile_name="balanced",
-        )
-
-        console.print("\n[bold green]✓ Cloud setup completed successfully![/bold green]")
-        console.print("\nYour cloud files are now accessible at:")
-        console.print(f"  {mount_path}")
-        console.print("\nYou can now edit files locally and they will sync to the cloud!")
-        console.print("\nUseful commands:")
-        console.print("  basic-memory cloud mount-status    # Check mount status")
-        console.print("  basic-memory cloud unmount         # Unmount files")
-        console.print("  basic-memory cloud mount --profile fast  # Remount with faster sync")
-
-    except (RcloneInstallError, MountError, CloudAPIError) as e:
-        console.print(f"\n[red]Setup failed: {e}[/red]")
-        raise typer.Exit(1)
-    except Exception as e:
-        console.print(f"\n[red]Unexpected error during setup: {e}[/red]")
-        raise typer.Exit(1)
-
-
-def mount_cloud_files(
-    tenant_id: Optional[str] = None,
-    bucket_name: Optional[str] = None,
-    mount_path: Optional[Path] = None,
-    profile_name: str = "balanced",
-) -> None:
-    """Mount cloud files with specified profile."""
-
-    try:
-        # Get tenant info if not provided
-        if not tenant_id or not bucket_name:
-            tenant_info = asyncio.run(get_tenant_info())
-            tenant_id = tenant_info.get("tenant_id")
-            bucket_name = tenant_info.get("bucket_name")
-
-            if not tenant_id or not bucket_name:
-                raise MountError("Could not determine tenant information")
-
-        # Set default mount path if not provided
-        if not mount_path:
-            mount_path = get_default_mount_path()
-
-        # Get mount profile
-        if profile_name not in MOUNT_PROFILES:
-            raise MountError(
-                f"Unknown profile: {profile_name}. Available: {list(MOUNT_PROFILES.keys())}"
-            )
-
-        profile = MOUNT_PROFILES[profile_name]
-
-        # Check if already mounted
-        if is_path_mounted(mount_path):
-            console.print(f"[yellow]Path {mount_path} is already mounted[/yellow]")
-            console.print("Use 'basic-memory cloud unmount' first, or mount to a different path")
-            return
-
-        # Create mount directory
-        mount_path.mkdir(parents=True, exist_ok=True)
-
-        # Build and execute mount command
-        mount_cmd = build_mount_command(tenant_id, bucket_name, mount_path, profile)
-
-        console.print(
-            f"[blue]Mounting with profile '{profile_name}' ({profile.description})...[/blue]"
-        )
-        console.print(f"[dim]Command: {' '.join(mount_cmd)}[/dim]")
-
-        result = subprocess.run(mount_cmd, capture_output=True, text=True)
-
-        if result.returncode != 0:
-            error_msg = result.stderr or "Unknown error"
-            raise MountError(f"Mount command failed: {error_msg}")
-
-        # Wait a moment for mount to establish
-        time.sleep(2)
-
-        # Verify mount
-        if is_path_mounted(mount_path):
-            console.print(f"[green]✓ Successfully mounted to {mount_path}[/green]")
-            console.print(f"[green]✓ Sync profile: {profile.description}[/green]")
-        else:
-            raise MountError("Mount command succeeded but path is not mounted")
-
-    except MountError:
-        raise
-    except Exception as e:
-        raise MountError(f"Unexpected error during mount: {e}") from e
-
-
-def unmount_cloud_files(tenant_id: Optional[str] = None) -> None:
-    """Unmount cloud files."""
-
-    try:
-        # Get tenant info if not provided
-        if not tenant_id:
-            tenant_info = asyncio.run(get_tenant_info())
-            tenant_id = tenant_info.get("tenant_id")
-
-            if not tenant_id:
-                raise MountError("Could not determine tenant ID")
-
-        mount_path = get_default_mount_path()
-
-        if not is_path_mounted(mount_path):
-            console.print(f"[yellow]Path {mount_path} is not mounted[/yellow]")
-            return
-
-        console.print(f"[blue]Unmounting {mount_path}...[/blue]")
-
-        # Unmount the path
-        if unmount_path(mount_path):
-            console.print(f"[green]✓ Successfully unmounted {mount_path}[/green]")
-
-            # Clean up any orphaned rclone processes
-            killed_count = cleanup_orphaned_rclone_processes()
-            if killed_count > 0:
-                console.print(
-                    f"[green]✓ Cleaned up {killed_count} orphaned rclone process(es)[/green]"
-                )
-        else:
-            console.print(f"[red]✗ Failed to unmount {mount_path}[/red]")
-            console.print("You may need to manually unmount or restart your system")
-
-    except MountError:
-        raise
-    except Exception as e:
-        raise MountError(f"Unexpected error during unmount: {e}") from e
-
-
-def show_mount_status() -> None:
-    """Show current mount status and running processes."""
-
-    try:
-        # Get tenant info
-        tenant_info = asyncio.run(get_tenant_info())
-        tenant_id = tenant_info.get("tenant_id")
-
-        if not tenant_id:
-            console.print("[red]Could not determine tenant ID[/red]")
-            return
-
-        mount_path = get_default_mount_path()
-
-        # Create status table
-        table = Table(title="Cloud Mount Status", show_header=True, header_style="bold blue")
-        table.add_column("Property", style="green", min_width=15)
-        table.add_column("Value", style="dim", min_width=30)
-
-        # Check mount status
-        is_mounted = is_path_mounted(mount_path)
-        mount_status = "[green]✓ Mounted[/green]" if is_mounted else "[red]✗ Not mounted[/red]"
-
-        table.add_row("Tenant ID", tenant_id)
-        table.add_row("Mount Path", str(mount_path))
-        table.add_row("Status", mount_status)
-
-        # Get rclone processes
-        processes = get_rclone_processes()
-        if processes:
-            table.add_row("rclone Processes", f"{len(processes)} running")
-        else:
-            table.add_row("rclone Processes", "None")
-
-        console.print(table)
-
-        # Show running processes details
-        if processes:
-            console.print("\n[bold]Running rclone processes:[/bold]")
-            for proc in processes:
-                console.print(f"  PID {proc['pid']}: {proc['command'][:80]}...")
-
-        # Show mount profiles
-        console.print("\n[bold]Available mount profiles:[/bold]")
-        for name, profile in MOUNT_PROFILES.items():
-            console.print(f"  {name}: {profile.description}")
-
-    except Exception as e:
-        console.print(f"[red]Error getting mount status: {e}[/red]")
-        raise typer.Exit(1)

src/basic_memory/cli/commands/cloud/rclone_commands.py

@@ -0,0 +1,326 @@
+"""Project-scoped rclone sync commands for Basic Memory Cloud.
+
+This module provides simplified, project-scoped rclone operations:
+- Each project syncs independently
+- Uses single "basic-memory-cloud" remote (not tenant-specific)
+- Balanced defaults from SPEC-8 Phase 4 testing
+- Per-project bisync state tracking
+
+Replaces tenant-wide sync with project-scoped workflows.
+"""
+
+import subprocess
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Optional
+
+from rich.console import Console
+
+from basic_memory.cli.commands.cloud.rclone_installer import is_rclone_installed
+from basic_memory.utils import normalize_project_path
+
+console = Console()
+
+
+class RcloneError(Exception):
+    """Exception raised for rclone command errors."""
+
+    pass
+
+
+def check_rclone_installed() -> None:
+    """Check if rclone is installed and raise helpful error if not.
+
+    Raises:
+        RcloneError: If rclone is not installed with installation instructions
+    """
+    if not is_rclone_installed():
+        raise RcloneError(
+            "rclone is not installed.\n\n"
+            "Install rclone by running: bm cloud setup\n"
+            "Or install manually from: https://rclone.org/downloads/\n\n"
+            "Windows users: Ensure you have a package manager installed (winget, chocolatey, or scoop)"
+        )
+
+
+@dataclass
+class SyncProject:
+    """Project configured for cloud sync.
+
+    Attributes:
+        name: Project name
+        path: Cloud path (e.g., "app/data/research")
+        local_sync_path: Local directory for syncing (optional)
+    """
+
+    name: str
+    path: str
+    local_sync_path: Optional[str] = None
+
+
+def get_bmignore_filter_path() -> Path:
+    """Get path to rclone filter file.
+
+    Uses ~/.basic-memory/.bmignore converted to rclone format.
+    File is automatically created with default patterns on first use.
+
+    Returns:
+        Path to rclone filter file
+    """
+    # Import here to avoid circular dependency
+    from basic_memory.cli.commands.cloud.bisync_commands import (
+        convert_bmignore_to_rclone_filters,
+    )
+
+    return convert_bmignore_to_rclone_filters()
+
+
+def get_project_bisync_state(project_name: str) -> Path:
+    """Get path to project's bisync state directory.
+
+    Args:
+        project_name: Name of the project
+
+    Returns:
+        Path to bisync state directory for this project
+    """
+    return Path.home() / ".basic-memory" / "bisync-state" / project_name
+
+
+def bisync_initialized(project_name: str) -> bool:
+    """Check if bisync has been initialized for this project.
+
+    Args:
+        project_name: Name of the project
+
+    Returns:
+        True if bisync state exists, False otherwise
+    """
+    state_path = get_project_bisync_state(project_name)
+    return state_path.exists() and any(state_path.iterdir())
+
+
+def get_project_remote(project: SyncProject, bucket_name: str) -> str:
+    """Build rclone remote path for project.
+
+    Args:
+        project: Project with cloud path
+        bucket_name: S3 bucket name
+
+    Returns:
+        Remote path like "basic-memory-cloud:bucket-name/basic-memory-llc"
+
+    Note:
+        The API returns paths like "/app/data/basic-memory-llc" because the S3 bucket
+        is mounted at /app/data on the fly machine. We need to strip the /app/data/
+        prefix to get the actual S3 path within the bucket.
+    """
+    # Normalize path to strip /app/data/ mount point prefix
+    cloud_path = normalize_project_path(project.path).lstrip("/")
+    return f"basic-memory-cloud:{bucket_name}/{cloud_path}"
+
+
+def project_sync(
+    project: SyncProject,
+    bucket_name: str,
+    dry_run: bool = False,
+    verbose: bool = False,
+) -> bool:
+    """One-way sync: local → cloud.
+
+    Makes cloud identical to local using rclone sync.
+
+    Args:
+        project: Project to sync
+        bucket_name: S3 bucket name
+        dry_run: Preview changes without applying
+        verbose: Show detailed output
+
+    Returns:
+        True if sync succeeded, False otherwise
+
+    Raises:
+        RcloneError: If project has no local_sync_path configured or rclone not installed
+    """
+    check_rclone_installed()
+
+    if not project.local_sync_path:
+        raise RcloneError(f"Project {project.name} has no local_sync_path configured")
+
+    local_path = Path(project.local_sync_path).expanduser()
+    remote_path = get_project_remote(project, bucket_name)
+    filter_path = get_bmignore_filter_path()
+
+    cmd = [
+        "rclone",
+        "sync",
+        str(local_path),
+        remote_path,
+        "--filter-from",
+        str(filter_path),
+    ]
+
+    if verbose:
+        cmd.append("--verbose")
+    else:
+        cmd.append("--progress")
+
+    if dry_run:
+        cmd.append("--dry-run")
+
+    result = subprocess.run(cmd, text=True)
+    return result.returncode == 0
+
+
+def project_bisync(
+    project: SyncProject,
+    bucket_name: str,
+    dry_run: bool = False,
+    resync: bool = False,
+    verbose: bool = False,
+) -> bool:
+    """Two-way sync: local ↔ cloud.
+
+    Uses rclone bisync with balanced defaults:
+    - conflict_resolve: newer (auto-resolve to most recent)
+    - max_delete: 25 (safety limit)
+    - compare: modtime (ignore size differences from line ending conversions)
+    - check_access: false (skip for performance)
+
+    Args:
+        project: Project to sync
+        bucket_name: S3 bucket name
+        dry_run: Preview changes without applying
+        resync: Force resync to establish new baseline
+        verbose: Show detailed output
+
+    Returns:
+        True if bisync succeeded, False otherwise
+
+    Raises:
+        RcloneError: If project has no local_sync_path, needs --resync, or rclone not installed
+    """
+    check_rclone_installed()
+
+    if not project.local_sync_path:
+        raise RcloneError(f"Project {project.name} has no local_sync_path configured")
+
+    local_path = Path(project.local_sync_path).expanduser()
+    remote_path = get_project_remote(project, bucket_name)
+    filter_path = get_bmignore_filter_path()
+    state_path = get_project_bisync_state(project.name)
+
+    # Ensure state directory exists
+    state_path.mkdir(parents=True, exist_ok=True)
+
+    cmd = [
+        "rclone",
+        "bisync",
+        str(local_path),
+        remote_path,
+        "--create-empty-src-dirs",
+        "--resilient",
+        "--conflict-resolve=newer",
+        "--max-delete=25",
+        "--compare=modtime",  # Ignore size differences from line ending conversions
+        "--filter-from",
+        str(filter_path),
+        "--workdir",
+        str(state_path),
+    ]
+
+    if verbose:
+        cmd.append("--verbose")
+    else:
+        cmd.append("--progress")
+
+    if dry_run:
+        cmd.append("--dry-run")
+
+    if resync:
+        cmd.append("--resync")
+
+    # Check if first run requires resync
+    if not resync and not bisync_initialized(project.name) and not dry_run:
+        raise RcloneError(
+            f"First bisync for {project.name} requires --resync to establish baseline.\n"
+            f"Run: bm project bisync --name {project.name} --resync"
+        )
+
+    result = subprocess.run(cmd, text=True)
+    return result.returncode == 0
+
+
+def project_check(
+    project: SyncProject,
+    bucket_name: str,
+    one_way: bool = False,
+) -> bool:
+    """Check integrity between local and cloud.
+
+    Verifies files match without transferring data.
+
+    Args:
+        project: Project to check
+        bucket_name: S3 bucket name
+        one_way: Only check for missing files on destination (faster)
+
+    Returns:
+        True if files match, False if differences found
+
+    Raises:
+        RcloneError: If project has no local_sync_path configured or rclone not installed
+    """
+    check_rclone_installed()
+
+    if not project.local_sync_path:
+        raise RcloneError(f"Project {project.name} has no local_sync_path configured")
+
+    local_path = Path(project.local_sync_path).expanduser()
+    remote_path = get_project_remote(project, bucket_name)
+    filter_path = get_bmignore_filter_path()
+
+    cmd = [
+        "rclone",
+        "check",
+        str(local_path),
+        remote_path,
+        "--filter-from",
+        str(filter_path),
+    ]
+
+    if one_way:
+        cmd.append("--one-way")
+
+    result = subprocess.run(cmd, capture_output=True, text=True)
+    return result.returncode == 0
+
+
+def project_ls(
+    project: SyncProject,
+    bucket_name: str,
+    path: Optional[str] = None,
+) -> list[str]:
+    """List files in remote project.
+
+    Args:
+        project: Project to list files from
+        bucket_name: S3 bucket name
+        path: Optional subdirectory within project
+
+    Returns:
+        List of file paths
+
+    Raises:
+        subprocess.CalledProcessError: If rclone command fails
+        RcloneError: If rclone is not installed
+    """
+    check_rclone_installed()
+
+    remote_path = get_project_remote(project, bucket_name)
+    if path:
+        remote_path = f"{remote_path}/{path}"
+
+    cmd = ["rclone", "ls", remote_path]
+    result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+    return result.stdout.splitlines()

src/basic_memory/cli/commands/cloud/rclone_config.py

@@ -1,11 +1,14 @@
-"""rclone configuration management for Basic Memory Cloud."""
+"""rclone configuration management for Basic Memory Cloud.
+
+This module provides simplified rclone configuration for SPEC-20.
+Uses a single "basic-memory-cloud" remote for all operations.
+"""
 
 import configparser
 import os
 import shutil
-import subprocess
 from pathlib import Path
-from typing import Dict, List, Optional
+from typing import Optional
 
 from rich.console import Console
 
@@ -18,64 +21,6 @@ class RcloneConfigError(Exception):
     pass
 
 
-class RcloneMountProfile:
-    """Mount profile with optimized settings."""
-
-    def __init__(
-        self,
-        name: str,
-        cache_time: str,
-        poll_interval: str,
-        attr_timeout: str,
-        write_back: str,
-        description: str,
-        extra_args: Optional[List[str]] = None,
-    ):
-        self.name = name
-        self.cache_time = cache_time
-        self.poll_interval = poll_interval
-        self.attr_timeout = attr_timeout
-        self.write_back = write_back
-        self.description = description
-        self.extra_args = extra_args or []
-
-
-# Mount profiles based on SPEC-7 Phase 4 testing
-MOUNT_PROFILES = {
-    "fast": RcloneMountProfile(
-        name="fast",
-        cache_time="5s",
-        poll_interval="3s",
-        attr_timeout="3s",
-        write_back="1s",
-        description="Ultra-fast development (5s sync, higher bandwidth)",
-    ),
-    "balanced": RcloneMountProfile(
-        name="balanced",
-        cache_time="10s",
-        poll_interval="5s",
-        attr_timeout="5s",
-        write_back="2s",
-        description="Fast development (10-15s sync, recommended)",
-    ),
-    "safe": RcloneMountProfile(
-        name="safe",
-        cache_time="15s",
-        poll_interval="10s",
-        attr_timeout="10s",
-        write_back="5s",
-        description="Conflict-aware mount with backup",
-        extra_args=[
-            "--conflict-suffix",
-            ".conflict-{DateTimeExt}",
-            "--backup-dir",
-            "~/.basic-memory/conflicts",
-            "--track-renames",
-        ],
-    ),
-}
-
-
 def get_rclone_config_path() -> Path:
     """Get the path to rclone configuration file."""
     config_dir = Path.home() / ".config" / "rclone"
@@ -116,173 +61,50 @@ def save_rclone_config(config: configparser.ConfigParser) -> None:
     console.print(f"[dim]Updated rclone config: {config_path}[/dim]")
 
 
-def add_tenant_to_rclone_config(
-    tenant_id: str,
-    bucket_name: str,
+def configure_rclone_remote(
     access_key: str,
     secret_key: str,
     endpoint: str = "https://fly.storage.tigris.dev",
     region: str = "auto",
 ) -> str:
-    """Add tenant configuration to rclone config file."""
+    """Configure single rclone remote named 'basic-memory-cloud'.
 
+    This is the simplified approach from SPEC-20 that uses one remote
+    for all Basic Memory cloud operations (not tenant-specific).
+
+    Args:
+        access_key: S3 access key ID
+        secret_key: S3 secret access key
+        endpoint: S3-compatible endpoint URL
+        region: S3 region (default: auto)
+
+    Returns:
+        The remote name: "basic-memory-cloud"
+    """
     # Backup existing config
     backup_rclone_config()
 
     # Load existing config
     config = load_rclone_config()
 
-    # Create section name
-    section_name = f"basic-memory-{tenant_id}"
+    # Single remote name (not tenant-specific)
+    REMOTE_NAME = "basic-memory-cloud"
 
-    # Add/update the tenant section
-    if not config.has_section(section_name):
-        config.add_section(section_name)
-
-    config.set(section_name, "type", "s3")
-    config.set(section_name, "provider", "Other")
-    config.set(section_name, "access_key_id", access_key)
-    config.set(section_name, "secret_access_key", secret_key)
-    config.set(section_name, "endpoint", endpoint)
-    config.set(section_name, "region", region)
+    # Add/update the remote section
+    if not config.has_section(REMOTE_NAME):
+        config.add_section(REMOTE_NAME)
 
+    config.set(REMOTE_NAME, "type", "s3")
+    config.set(REMOTE_NAME, "provider", "Other")
+    config.set(REMOTE_NAME, "access_key_id", access_key)
+    config.set(REMOTE_NAME, "secret_access_key", secret_key)
+    config.set(REMOTE_NAME, "endpoint", endpoint)
+    config.set(REMOTE_NAME, "region", region)
+    # Prevent unnecessary encoding of filenames (only encode slashes and invalid UTF-8)
+    # This prevents files with spaces like "Hello World.md" from being quoted
+    config.set(REMOTE_NAME, "encoding", "Slash,InvalidUtf8")
     # Save updated config
     save_rclone_config(config)
 
-    console.print(f"[green]✓ Added tenant {tenant_id} to rclone config[/green]")
-    return section_name
-
-
-def remove_tenant_from_rclone_config(tenant_id: str) -> bool:
-    """Remove tenant configuration from rclone config."""
-    config = load_rclone_config()
-    section_name = f"basic-memory-{tenant_id}"
-
-    if config.has_section(section_name):
-        backup_rclone_config()
-        config.remove_section(section_name)
-        save_rclone_config(config)
-        console.print(f"[green]✓ Removed tenant {tenant_id} from rclone config[/green]")
-        return True
-
-    return False
-
-
-def get_default_mount_path() -> Path:
-    """Get default mount path (fixed location per SPEC-9).
-
-    Returns:
-        Fixed mount path: ~/basic-memory-cloud/
-    """
-    return Path.home() / "basic-memory-cloud"
-
-
-def build_mount_command(
-    tenant_id: str, bucket_name: str, mount_path: Path, profile: RcloneMountProfile
-) -> List[str]:
-    """Build rclone mount command with optimized settings."""
-
-    rclone_remote = f"basic-memory-{tenant_id}:{bucket_name}"
-
-    cmd = [
-        "rclone",
-        "nfsmount",
-        rclone_remote,
-        str(mount_path),
-        "--vfs-cache-mode",
-        "writes",
-        "--dir-cache-time",
-        profile.cache_time,
-        "--vfs-cache-poll-interval",
-        profile.poll_interval,
-        "--attr-timeout",
-        profile.attr_timeout,
-        "--vfs-write-back",
-        profile.write_back,
-        "--daemon",
-    ]
-
-    # Add profile-specific extra arguments
-    cmd.extend(profile.extra_args)
-
-    return cmd
-
-
-def is_path_mounted(mount_path: Path) -> bool:
-    """Check if a path is currently mounted."""
-    if not mount_path.exists():
-        return False
-
-    try:
-        # Check if mount point is actually mounted by looking for mount table entry
-        result = subprocess.run(["mount"], capture_output=True, text=True, check=False)
-
-        if result.returncode == 0:
-            # Look for our mount path in mount output
-            mount_str = str(mount_path.resolve())
-            return mount_str in result.stdout
-
-        return False
-    except Exception:
-        return False
-
-
-def get_rclone_processes() -> List[Dict[str, str]]:
-    """Get list of running rclone processes."""
-    try:
-        # Use ps to find rclone processes
-        result = subprocess.run(
-            ["ps", "-eo", "pid,args"], capture_output=True, text=True, check=False
-        )
-
-        processes = []
-        if result.returncode == 0:
-            for line in result.stdout.split("\n"):
-                if "rclone" in line and "basic-memory" in line:
-                    parts = line.strip().split(None, 1)
-                    if len(parts) >= 2:
-                        processes.append({"pid": parts[0], "command": parts[1]})
-
-        return processes
-    except Exception:
-        return []
-
-
-def kill_rclone_process(pid: str) -> bool:
-    """Kill a specific rclone process."""
-    try:
-        subprocess.run(["kill", pid], check=True)
-        console.print(f"[green]✓ Killed rclone process {pid}[/green]")
-        return True
-    except subprocess.CalledProcessError:
-        console.print(f"[red]✗ Failed to kill rclone process {pid}[/red]")
-        return False
-
-
-def unmount_path(mount_path: Path) -> bool:
-    """Unmount a mounted path."""
-    if not is_path_mounted(mount_path):
-        return True
-
-    try:
-        subprocess.run(["umount", str(mount_path)], check=True)
-        console.print(f"[green]✓ Unmounted {mount_path}[/green]")
-        return True
-    except subprocess.CalledProcessError as e:
-        console.print(f"[red]✗ Failed to unmount {mount_path}: {e}[/red]")
-        return False
-
-
-def cleanup_orphaned_rclone_processes() -> int:
-    """Clean up orphaned rclone processes for basic-memory."""
-    processes = get_rclone_processes()
-    killed_count = 0
-
-    for proc in processes:
-        console.print(
-            f"[yellow]Found rclone process: {proc['pid']} - {proc['command'][:80]}...[/yellow]"
-        )
-        if kill_rclone_process(proc["pid"]):
-            killed_count += 1
-
-    return killed_count
+    console.print(f"[green]Configured rclone remote: {REMOTE_NAME}[/green]")
+    return REMOTE_NAME

src/basic_memory/cli/commands/cloud/rclone_installer.py

@@ -1,5 +1,6 @@
 """Cross-platform rclone installation utilities."""
 
+import os
 import platform
 import shutil
 import subprocess
@@ -58,7 +59,7 @@ def install_rclone_macos() -> None:
         try:
             console.print("[blue]Installing rclone via Homebrew...[/blue]")
             run_command(["brew", "install", "rclone"])
-            console.print("[green]✓ rclone installed via Homebrew[/green]")
+            console.print("[green]rclone installed via Homebrew[/green]")
             return
         except RcloneInstallError:
             console.print(
@@ -69,7 +70,7 @@ def install_rclone_macos() -> None:
     console.print("[blue]Installing rclone via official script...[/blue]")
     try:
         run_command(["sh", "-c", "curl https://rclone.org/install.sh | sudo bash"])
-        console.print("[green]✓ rclone installed via official script[/green]")
+        console.print("[green]rclone installed via official script[/green]")
     except RcloneInstallError:
         raise RcloneInstallError(
             "Failed to install rclone. Please install manually: brew install rclone"
@@ -83,7 +84,7 @@ def install_rclone_linux() -> None:
         try:
             console.print("[blue]Installing rclone via snap...[/blue]")
             run_command(["sudo", "snap", "install", "rclone"])
-            console.print("[green]✓ rclone installed via snap[/green]")
+            console.print("[green]rclone installed via snap[/green]")
             return
         except RcloneInstallError:
             console.print("[yellow]Snap installation failed, trying apt...[/yellow]")
@@ -94,7 +95,7 @@ def install_rclone_linux() -> None:
             console.print("[blue]Installing rclone via apt...[/blue]")
             run_command(["sudo", "apt", "update"])
             run_command(["sudo", "apt", "install", "-y", "rclone"])
-            console.print("[green]✓ rclone installed via apt[/green]")
+            console.print("[green]rclone installed via apt[/green]")
             return
         except RcloneInstallError:
             console.print("[yellow]apt installation failed, trying official script...[/yellow]")
@@ -103,7 +104,7 @@ def install_rclone_linux() -> None:
     console.print("[blue]Installing rclone via official script...[/blue]")
     try:
         run_command(["sh", "-c", "curl https://rclone.org/install.sh | sudo bash"])
-        console.print("[green]✓ rclone installed via official script[/green]")
+        console.print("[green]rclone installed via official script[/green]")
     except RcloneInstallError:
         raise RcloneInstallError(
             "Failed to install rclone. Please install manually: sudo snap install rclone"
@@ -116,8 +117,16 @@ def install_rclone_windows() -> None:
     if shutil.which("winget"):
         try:
             console.print("[blue]Installing rclone via winget...[/blue]")
-            run_command(["winget", "install", "Rclone.Rclone"])
-            console.print("[green]✓ rclone installed via winget[/green]")
+            run_command(
+                [
+                    "winget",
+                    "install",
+                    "Rclone.Rclone",
+                    "--accept-source-agreements",
+                    "--accept-package-agreements",
+                ]
+            )
+            console.print("[green]rclone installed via winget[/green]")
             return
         except RcloneInstallError:
             console.print("[yellow]winget installation failed, trying chocolatey...[/yellow]")
@@ -127,7 +136,7 @@ def install_rclone_windows() -> None:
         try:
             console.print("[blue]Installing rclone via chocolatey...[/blue]")
             run_command(["choco", "install", "rclone", "-y"])
-            console.print("[green]✓ rclone installed via chocolatey[/green]")
+            console.print("[green]rclone installed via chocolatey[/green]")
             return
         except RcloneInstallError:
             console.print("[yellow]chocolatey installation failed, trying scoop...[/yellow]")
@@ -137,16 +146,30 @@ def install_rclone_windows() -> None:
         try:
             console.print("[blue]Installing rclone via scoop...[/blue]")
             run_command(["scoop", "install", "rclone"])
-            console.print("[green]✓ rclone installed via scoop[/green]")
+            console.print("[green]rclone installed via scoop[/green]")
             return
         except RcloneInstallError:
             console.print("[yellow]scoop installation failed[/yellow]")
 
-    # No package manager available
-    raise RcloneInstallError(
-        "Could not install rclone automatically. Please install a package manager "
-        "(winget, chocolatey, or scoop) or install rclone manually from https://rclone.org/downloads/"
+    # No package manager available - provide detailed instructions
+    error_msg = (
+        "Could not install rclone automatically.\n\n"
+        "Windows requires a package manager to install rclone. Options:\n\n"
+        "1. Install winget (recommended, built into Windows 11):\n"
+        "   - Windows 11: Already installed\n"
+        "   - Windows 10: Install 'App Installer' from Microsoft Store\n"
+        "   - Then run: bm cloud setup\n\n"
+        "2. Install chocolatey:\n"
+        "   - Visit: https://chocolatey.org/install\n"
+        "   - Then run: bm cloud setup\n\n"
+        "3. Install scoop:\n"
+        "   - Visit: https://scoop.sh\n"
+        "   - Then run: bm cloud setup\n\n"
+        "4. Manual installation:\n"
+        "   - Download from: https://rclone.org/downloads/\n"
+        "   - Extract and add to PATH\n"
     )
+    raise RcloneInstallError(error_msg)
 
 
 def install_rclone(platform_override: Optional[str] = None) -> None:
@@ -165,6 +188,7 @@ def install_rclone(platform_override: Optional[str] = None) -> None:
             install_rclone_linux()
         elif platform_name == "windows":
             install_rclone_windows()
+            refresh_windows_path()
         else:
             raise RcloneInstallError(f"Unsupported platform: {platform_name}")
 
@@ -172,7 +196,7 @@ def install_rclone(platform_override: Optional[str] = None) -> None:
         if not is_rclone_installed():
             raise RcloneInstallError("rclone installation completed but command not found in PATH")
 
-        console.print("[green]✓ rclone installation completed successfully[/green]")
+        console.print("[green]rclone installation completed successfully[/green]")
 
     except RcloneInstallError:
         raise
@@ -180,6 +204,47 @@ def install_rclone(platform_override: Optional[str] = None) -> None:
         raise RcloneInstallError(f"Unexpected error during installation: {e}") from e
 
 
+def refresh_windows_path() -> None:
+    """Refresh the Windows PATH environment variable for the current session."""
+    if platform.system().lower() != "windows":
+        return
+
+    # Importing here after performing platform detection. Also note that we have to ignore pylance/pyright
+    # warnings about winreg attributes so that "errors" don't appear on non-Windows platforms.
+    import winreg
+
+    user_key_path = r"Environment"
+    system_key_path = r"System\CurrentControlSet\Control\Session Manager\Environment"
+    new_path = ""
+
+    # Read user PATH
+    try:
+        reg_key = winreg.OpenKey(winreg.HKEY_CURRENT_USER, user_key_path, 0, winreg.KEY_READ)  # type: ignore[reportAttributeAccessIssue]
+        user_path, _ = winreg.QueryValueEx(reg_key, "PATH")  # type: ignore[reportAttributeAccessIssue]
+        winreg.CloseKey(reg_key)  # type: ignore[reportAttributeAccessIssue]
+    except Exception:
+        user_path = ""
+
+    # Read system PATH
+    try:
+        reg_key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, system_key_path, 0, winreg.KEY_READ)  # type: ignore[reportAttributeAccessIssue]
+        system_path, _ = winreg.QueryValueEx(reg_key, "PATH")  # type: ignore[reportAttributeAccessIssue]
+        winreg.CloseKey(reg_key)  # type: ignore[reportAttributeAccessIssue]
+    except Exception:
+        system_path = ""
+
+    # Merge user and system PATHs (system first, then user)
+    if system_path and user_path:
+        new_path = system_path + ";" + user_path
+    elif system_path:
+        new_path = system_path
+    elif user_path:
+        new_path = user_path
+
+    if new_path:
+        os.environ["PATH"] = new_path
+
+
 def get_rclone_version() -> Optional[str]:
     """Get the installed rclone version."""
     if not is_rclone_installed():

src/basic_memory/cli/commands/cloud/upload.py

@@ -0,0 +1,233 @@
+"""WebDAV upload functionality for basic-memory projects."""
+
+import os
+from pathlib import Path
+
+import aiofiles
+import httpx
+
+from basic_memory.ignore_utils import load_gitignore_patterns, should_ignore_path
+from basic_memory.mcp.async_client import get_client
+from basic_memory.mcp.tools.utils import call_put
+
+# Archive file extensions that should be skipped during upload
+ARCHIVE_EXTENSIONS = {".zip", ".tar", ".gz", ".bz2", ".xz", ".7z", ".rar", ".tgz", ".tbz2"}
+
+
+async def upload_path(
+    local_path: Path,
+    project_name: str,
+    verbose: bool = False,
+    use_gitignore: bool = True,
+    dry_run: bool = False,
+) -> bool:
+    """
+    Upload a file or directory to cloud project via WebDAV.
+
+    Args:
+        local_path: Path to local file or directory
+        project_name: Name of cloud project (destination)
+        verbose: Show detailed information about filtering and upload
+        use_gitignore: If False, skip .gitignore patterns (still use .bmignore)
+        dry_run: If True, show what would be uploaded without uploading
+
+    Returns:
+        True if upload succeeded, False otherwise
+    """
+    try:
+        # Resolve path
+        local_path = local_path.resolve()
+
+        # Check if path exists
+        if not local_path.exists():
+            print(f"Error: Path does not exist: {local_path}")
+            return False
+
+        # Get files to upload
+        if local_path.is_file():
+            files_to_upload = [(local_path, local_path.name)]
+            if verbose:
+                print(f"Uploading single file: {local_path.name}")
+        else:
+            files_to_upload = _get_files_to_upload(local_path, verbose, use_gitignore)
+
+        if not files_to_upload:
+            print("No files found to upload")
+            if verbose:
+                print(
+                    "\nTip: Use --verbose to see which files are being filtered, "
+                    "or --no-gitignore to skip .gitignore patterns"
+                )
+            return True
+
+        print(f"Found {len(files_to_upload)} file(s) to upload")
+
+        # Calculate total size
+        total_bytes = sum(file_path.stat().st_size for file_path, _ in files_to_upload)
+        skipped_count = 0
+
+        # If dry run, just show what would be uploaded
+        if dry_run:
+            print("\nFiles that would be uploaded:")
+            for file_path, relative_path in files_to_upload:
+                # Skip archive files
+                if _is_archive_file(file_path):
+                    print(f"  [SKIP] {relative_path} (archive file)")
+                    skipped_count += 1
+                    continue
+
+                size = file_path.stat().st_size
+                if size < 1024:
+                    size_str = f"{size} bytes"
+                elif size < 1024 * 1024:
+                    size_str = f"{size / 1024:.1f} KB"
+                else:
+                    size_str = f"{size / (1024 * 1024):.1f} MB"
+                print(f"  {relative_path} ({size_str})")
+        else:
+            # Upload files using httpx
+            async with get_client() as client:
+                for i, (file_path, relative_path) in enumerate(files_to_upload, 1):
+                    # Skip archive files (zip, tar, gz, etc.)
+                    if _is_archive_file(file_path):
+                        print(
+                            f"Skipping archive file: {relative_path} ({i}/{len(files_to_upload)})"
+                        )
+                        skipped_count += 1
+                        continue
+
+                    # Build remote path: /webdav/{project_name}/{relative_path}
+                    remote_path = f"/webdav/{project_name}/{relative_path}"
+                    print(f"Uploading {relative_path} ({i}/{len(files_to_upload)})")
+
+                    # Get file modification time
+                    file_stat = file_path.stat()
+                    mtime = int(file_stat.st_mtime)
+
+                    # Read file content asynchronously
+                    async with aiofiles.open(file_path, "rb") as f:
+                        content = await f.read()
+
+                    # Upload via HTTP PUT to WebDAV endpoint with mtime header
+                    # Using X-OC-Mtime (ownCloud/Nextcloud standard)
+                    response = await call_put(
+                        client, remote_path, content=content, headers={"X-OC-Mtime": str(mtime)}
+                    )
+                    response.raise_for_status()
+
+        # Format total size based on magnitude
+        if total_bytes < 1024:
+            size_str = f"{total_bytes} bytes"
+        elif total_bytes < 1024 * 1024:
+            size_str = f"{total_bytes / 1024:.1f} KB"
+        else:
+            size_str = f"{total_bytes / (1024 * 1024):.1f} MB"
+
+        uploaded_count = len(files_to_upload) - skipped_count
+        if dry_run:
+            print(f"\nTotal: {uploaded_count} file(s) ({size_str})")
+            if skipped_count > 0:
+                print(f"  Would skip {skipped_count} archive file(s)")
+        else:
+            print(f"✓ Upload complete: {uploaded_count} file(s) ({size_str})")
+            if skipped_count > 0:
+                print(f"  Skipped {skipped_count} archive file(s)")
+
+        return True
+
+    except httpx.HTTPStatusError as e:
+        print(f"Upload failed: HTTP {e.response.status_code} - {e.response.text}")
+        return False
+    except Exception as e:
+        print(f"Upload failed: {e}")
+        return False
+
+
+def _is_archive_file(file_path: Path) -> bool:
+    """
+    Check if a file is an archive file based on its extension.
+
+    Args:
+        file_path: Path to the file to check
+
+    Returns:
+        True if file is an archive, False otherwise
+    """
+    return file_path.suffix.lower() in ARCHIVE_EXTENSIONS
+
+
+def _get_files_to_upload(
+    directory: Path, verbose: bool = False, use_gitignore: bool = True
+) -> list[tuple[Path, str]]:
+    """
+    Get list of files to upload from directory.
+
+    Uses .bmignore and optionally .gitignore patterns for filtering.
+
+    Args:
+        directory: Directory to scan
+        verbose: Show detailed filtering information
+        use_gitignore: If False, skip .gitignore patterns (still use .bmignore)
+
+    Returns:
+        List of (absolute_path, relative_path) tuples
+    """
+    files = []
+    ignored_files = []
+
+    # Load ignore patterns from .bmignore and optionally .gitignore
+    ignore_patterns = load_gitignore_patterns(directory, use_gitignore=use_gitignore)
+
+    if verbose:
+        gitignore_path = directory / ".gitignore"
+        gitignore_exists = gitignore_path.exists() and use_gitignore
+        print(f"\nScanning directory: {directory}")
+        print("Using .bmignore: Yes")
+        print(f"Using .gitignore: {'Yes' if gitignore_exists else 'No'}")
+        print(f"Ignore patterns loaded: {len(ignore_patterns)}")
+        if ignore_patterns and len(ignore_patterns) <= 20:
+            print(f"Patterns: {', '.join(sorted(ignore_patterns))}")
+        print()
+
+    # Walk through directory
+    for root, dirs, filenames in os.walk(directory):
+        root_path = Path(root)
+
+        # Filter directories based on ignore patterns
+        filtered_dirs = []
+        for d in dirs:
+            dir_path = root_path / d
+            if should_ignore_path(dir_path, directory, ignore_patterns):
+                if verbose:
+                    rel_path = dir_path.relative_to(directory)
+                    print(f"  [IGNORED DIR] {rel_path}/")
+            else:
+                filtered_dirs.append(d)
+        dirs[:] = filtered_dirs
+
+        # Process files
+        for filename in filenames:
+            file_path = root_path / filename
+
+            # Calculate relative path for display/remote
+            rel_path = file_path.relative_to(directory)
+            remote_path = str(rel_path).replace("\\", "/")
+
+            # Check if file should be ignored
+            if should_ignore_path(file_path, directory, ignore_patterns):
+                ignored_files.append(remote_path)
+                if verbose:
+                    print(f"  [IGNORED] {remote_path}")
+                continue
+
+            if verbose:
+                print(f"  [INCLUDE] {remote_path}")
+
+            files.append((file_path, remote_path))
+
+    if verbose:
+        print("\nSummary:")
+        print(f"  Files to upload: {len(files)}")
+        print(f"  Files ignored: {len(ignored_files)}")
+
+    return files

src/basic_memory/cli/commands/cloud/upload_command.py

@@ -0,0 +1,124 @@
+"""Upload CLI commands for basic-memory projects."""
+
+import asyncio
+from pathlib import Path
+
+import typer
+from rich.console import Console
+
+from basic_memory.cli.app import cloud_app
+from basic_memory.cli.commands.cloud.cloud_utils import (
+    create_cloud_project,
+    project_exists,
+    sync_project,
+)
+from basic_memory.cli.commands.cloud.upload import upload_path
+
+console = Console()
+
+
+@cloud_app.command("upload")
+def upload(
+    path: Path = typer.Argument(
+        ...,
+        help="Path to local file or directory to upload",
+        exists=True,
+        readable=True,
+        resolve_path=True,
+    ),
+    project: str = typer.Option(
+        ...,
+        "--project",
+        "-p",
+        help="Cloud project name (destination)",
+    ),
+    create_project: bool = typer.Option(
+        False,
+        "--create-project",
+        "-c",
+        help="Create project if it doesn't exist",
+    ),
+    sync: bool = typer.Option(
+        True,
+        "--sync/--no-sync",
+        help="Sync project after upload (default: true)",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "--verbose",
+        "-v",
+        help="Show detailed information about file filtering and upload",
+    ),
+    no_gitignore: bool = typer.Option(
+        False,
+        "--no-gitignore",
+        help="Skip .gitignore patterns (still respects .bmignore)",
+    ),
+    dry_run: bool = typer.Option(
+        False,
+        "--dry-run",
+        help="Show what would be uploaded without actually uploading",
+    ),
+) -> None:
+    """Upload local files or directories to cloud project via WebDAV.
+
+    Examples:
+      bm cloud upload ~/my-notes --project research
+      bm cloud upload notes.md --project research --create-project
+      bm cloud upload ~/docs --project work --no-sync
+      bm cloud upload ./history --project proto --verbose
+      bm cloud upload ./notes --project work --no-gitignore
+      bm cloud upload ./files --project test --dry-run
+    """
+
+    async def _upload():
+        # Check if project exists
+        if not await project_exists(project):
+            if create_project:
+                console.print(f"[blue]Creating cloud project '{project}'...[/blue]")
+                try:
+                    await create_cloud_project(project)
+                    console.print(f"[green]Created project '{project}'[/green]")
+                except Exception as e:
+                    console.print(f"[red]Failed to create project: {e}[/red]")
+                    raise typer.Exit(1)
+            else:
+                console.print(
+                    f"[red]Project '{project}' does not exist.[/red]\n"
+                    f"[yellow]Options:[/yellow]\n"
+                    f"  1. Create it first: bm project add {project}\n"
+                    f"  2. Use --create-project flag to create automatically"
+                )
+                raise typer.Exit(1)
+
+        # Perform upload (or dry run)
+        if dry_run:
+            console.print(
+                f"[yellow]DRY RUN: Showing what would be uploaded to '{project}'[/yellow]"
+            )
+        else:
+            console.print(f"[blue]Uploading {path} to project '{project}'...[/blue]")
+
+        success = await upload_path(
+            path, project, verbose=verbose, use_gitignore=not no_gitignore, dry_run=dry_run
+        )
+        if not success:
+            console.print("[red]Upload failed[/red]")
+            raise typer.Exit(1)
+
+        if dry_run:
+            console.print("[yellow]DRY RUN complete - no files were uploaded[/yellow]")
+        else:
+            console.print(f"[green]Successfully uploaded to '{project}'[/green]")
+
+        # Sync project if requested (skip on dry run)
+        # Force full scan after bisync to ensure database is up-to-date with synced files
+        if sync and not dry_run:
+            console.print(f"[blue]Syncing project '{project}'...[/blue]")
+            try:
+                await sync_project(project, force_full=True)
+            except Exception as e:
+                console.print(f"[yellow]Warning: Sync failed: {e}[/yellow]")
+                console.print("[dim]Files uploaded but may not be indexed yet[/dim]")
+
+    asyncio.run(_upload())

src/basic_memory/cli/commands/command_utils.py

@@ -16,17 +16,25 @@ from basic_memory.schemas import ProjectInfoResponse
 console = Console()
 
 
-async def run_sync(project: Optional[str] = None):
-    """Run sync operation via API endpoint."""
+async def run_sync(project: Optional[str] = None, force_full: bool = False):
+    """Run sync operation via API endpoint.
+
+    Args:
+        project: Optional project name
+        force_full: If True, force a full scan bypassing watermark optimization
+    """
 
     try:
         async with get_client() as client:
             project_item = await get_active_project(client, project, None)
-            response = await call_post(client, f"{project_item.project_url}/project/sync")
+            url = f"{project_item.project_url}/project/sync"
+            if force_full:
+                url += "?force_full=true"
+            response = await call_post(client, url)
             data = response.json()
-            console.print(f"[green]✓ {data['message']}[/green]")
+            console.print(f"[green]{data['message']}[/green]")
     except (ToolError, ValueError) as e:
-        console.print(f"[red]✗ Sync failed: {e}[/red]")
+        console.print(f"[red]Sync failed: {e}[/red]")
         raise typer.Exit(1)
 
 
@@ -39,5 +47,5 @@ async def get_project_info(project: str):
             response = await call_get(client, f"{project_item.project_url}/project/info")
             return ProjectInfoResponse.model_validate(response.json())
     except (ToolError, ValueError) as e:
-        console.print(f"[red]✗ Sync failed: {e}[/red]")
+        console.print(f"[red]Sync failed: {e}[/red]")
         raise typer.Exit(1)

src/basic_memory/cli/commands/db.py

@@ -37,8 +37,8 @@ def reset(
         logger.info("Database reset complete")
 
         if reindex:
-            # Import and run sync
-            from basic_memory.cli.commands.sync import sync
+            # Run database sync directly
+            from basic_memory.cli.commands.command_utils import run_sync
 
             logger.info("Rebuilding search index from filesystem...")
-            sync(watch=False)  # pyright: ignore
+            asyncio.run(run_sync(project=None))

src/basic_memory/cli/commands/project.py

@@ -22,17 +22,26 @@ from basic_memory.mcp.tools.utils import call_post
 from basic_memory.schemas.project_info import ProjectStatusResponse
 from basic_memory.mcp.tools.utils import call_delete
 from basic_memory.mcp.tools.utils import call_put
-from basic_memory.utils import generate_permalink
+from basic_memory.utils import generate_permalink, normalize_project_path
 from basic_memory.mcp.tools.utils import call_patch
 
+# Import rclone commands for project sync
+from basic_memory.cli.commands.cloud.rclone_commands import (
+    SyncProject,
+    RcloneError,
+    project_sync,
+    project_bisync,
+    project_check,
+    project_ls,
+)
+from basic_memory.cli.commands.cloud.bisync_commands import get_mount_info
+
 console = Console()
 
 # Create a project subcommand
 project_app = typer.Typer(help="Manage multiple Basic Memory projects")
 app.add_typer(project_app, name="project")
 
-config = ConfigManager().config
-
 
 def format_path(path: str) -> str:
     """Format a path for display, using ~ for home directory."""
@@ -53,15 +62,41 @@ def list_projects() -> None:
 
     try:
         result = asyncio.run(_list_projects())
+        config = ConfigManager().config
 
         table = Table(title="Basic Memory Projects")
         table.add_column("Name", style="cyan")
         table.add_column("Path", style="green")
-        table.add_column("Default", style="magenta")
+
+        # Add Local Path column if in cloud mode
+        if config.cloud_mode_enabled:
+            table.add_column("Local Path", style="yellow", no_wrap=True, overflow="fold")
+
+        # Show Default column in local mode or if default_project_mode is enabled in cloud mode
+        show_default_column = not config.cloud_mode_enabled or config.default_project_mode
+        if show_default_column:
+            table.add_column("Default", style="magenta")
 
         for project in result.projects:
-            is_default = "✓" if project.is_default else ""
-            table.add_row(project.name, format_path(project.path), is_default)
+            is_default = "[X]" if project.is_default else ""
+            normalized_path = normalize_project_path(project.path)
+
+            # Build row based on mode
+            row = [project.name, format_path(normalized_path)]
+
+            # Add local path if in cloud mode
+            if config.cloud_mode_enabled:
+                local_path = ""
+                if project.name in config.cloud_projects:
+                    local_path = config.cloud_projects[project.name].local_path or ""
+                    local_path = format_path(local_path)
+                row.append(local_path)
+
+            # Add default indicator if showing default column
+            if show_default_column:
+                row.append(is_default)
+
+            table.add_row(*row)
 
         console.print(table)
     except Exception as e:
@@ -69,40 +104,52 @@ def list_projects() -> None:
         raise typer.Exit(1)
 
 
-if config.cloud_mode_enabled:
+@project_app.command("add")
+def add_project(
+    name: str = typer.Argument(..., help="Name of the project"),
+    path: str = typer.Argument(
+        None, help="Path to the project directory (required for local mode)"
+    ),
+    local_path: str = typer.Option(
+        None, "--local-path", help="Local sync path for cloud mode (optional)"
+    ),
+    set_default: bool = typer.Option(False, "--default", help="Set as default project"),
+) -> None:
+    """Add a new project.
 
-    @project_app.command("add")
-    def add_project_cloud(
-        name: str = typer.Argument(..., help="Name of the project"),
-        set_default: bool = typer.Option(False, "--default", help="Set as default project"),
-    ) -> None:
-        """Add a new project to Basic Memory Cloud"""
+    Cloud mode examples:\n
+        bm project add research                           # No local sync\n
+        bm project add research --local-path ~/docs       # With local sync\n
+
+    Local mode example:\n
+        bm project add research ~/Documents/research
+    """
+    config = ConfigManager().config
+
+    # Resolve local sync path early (needed for both cloud and local mode)
+    local_sync_path: str | None = None
+    if local_path:
+        local_sync_path = Path(os.path.abspath(os.path.expanduser(local_path))).as_posix()
+
+    if config.cloud_mode_enabled:
+        # Cloud mode: path auto-generated from name, local sync is optional
 
         async def _add_project():
             async with get_client() as client:
-                data = {"name": name, "path": generate_permalink(name), "set_default": set_default}
+                data = {
+                    "name": name,
+                    "path": generate_permalink(name),
+                    "local_sync_path": local_sync_path,
+                    "set_default": set_default,
+                }
                 response = await call_post(client, "/projects/projects", json=data)
                 return ProjectStatusResponse.model_validate(response.json())
-
-        try:
-            result = asyncio.run(_add_project())
-            console.print(f"[green]{result.message}[/green]")
-        except Exception as e:
-            console.print(f"[red]Error adding project: {str(e)}[/red]")
+    else:
+        # Local mode: path is required
+        if path is None:
+            console.print("[red]Error: path argument is required in local mode[/red]")
             raise typer.Exit(1)
 
-        # Display usage hint
-        console.print("\nTo use this project:")
-        console.print(f"  basic-memory --project={name} <command>")
-else:
-
-    @project_app.command("add")
-    def add_project(
-        name: str = typer.Argument(..., help="Name of the project"),
-        path: str = typer.Argument(..., help="Path to the project directory"),
-        set_default: bool = typer.Option(False, "--default", help="Set as default project"),
-    ) -> None:
-        """Add a new project."""
         # Resolve to absolute path
         resolved_path = Path(os.path.abspath(os.path.expanduser(path))).as_posix()
 
@@ -112,119 +159,608 @@ else:
                 response = await call_post(client, "/projects/projects", json=data)
                 return ProjectStatusResponse.model_validate(response.json())
 
-        try:
-            result = asyncio.run(_add_project())
-            console.print(f"[green]{result.message}[/green]")
-        except Exception as e:
-            console.print(f"[red]Error adding project: {str(e)}[/red]")
-            raise typer.Exit(1)
+    try:
+        result = asyncio.run(_add_project())
+        console.print(f"[green]{result.message}[/green]")
 
-        # Display usage hint
-        console.print("\nTo use this project:")
-        console.print(f"  basic-memory --project={name} <command>")
+        # Save local sync path to config if in cloud mode
+        if config.cloud_mode_enabled and local_sync_path:
+            from basic_memory.config import CloudProjectConfig
+
+            # Create local directory if it doesn't exist
+            local_dir = Path(local_sync_path)
+            local_dir.mkdir(parents=True, exist_ok=True)
+
+            # Update config with sync path
+            config.cloud_projects[name] = CloudProjectConfig(
+                local_path=local_sync_path,
+                last_sync=None,
+                bisync_initialized=False,
+            )
+            ConfigManager().save_config(config)
+
+            console.print(f"\n[green]Local sync path configured: {local_sync_path}[/green]")
+            console.print("\nNext steps:")
+            console.print(f"  1. Preview: bm project bisync --name {name} --resync --dry-run")
+            console.print(f"  2. Sync: bm project bisync --name {name} --resync")
+    except Exception as e:
+        console.print(f"[red]Error adding project: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("sync-setup")
+def setup_project_sync(
+    name: str = typer.Argument(..., help="Project name"),
+    local_path: str = typer.Argument(..., help="Local sync directory"),
+) -> None:
+    """Configure local sync for an existing cloud project.
+
+    Example:
+      bm project sync-setup research ~/Documents/research
+    """
+    config_manager = ConfigManager()
+    config = config_manager.config
+
+    if not config.cloud_mode_enabled:
+        console.print("[red]Error: sync-setup only available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    async def _verify_project_exists():
+        """Verify the project exists on cloud by listing all projects."""
+        async with get_client() as client:
+            response = await call_get(client, "/projects/projects")
+            project_list = response.json()
+            project_names = [p["name"] for p in project_list["projects"]]
+            if name not in project_names:
+                raise ValueError(f"Project '{name}' not found on cloud")
+            return True
+
+    try:
+        # Verify project exists on cloud
+        asyncio.run(_verify_project_exists())
+
+        # Resolve and create local path
+        resolved_path = Path(os.path.abspath(os.path.expanduser(local_path)))
+        resolved_path.mkdir(parents=True, exist_ok=True)
+
+        # Update local config with sync path
+        from basic_memory.config import CloudProjectConfig
+
+        config.cloud_projects[name] = CloudProjectConfig(
+            local_path=resolved_path.as_posix(),
+            last_sync=None,
+            bisync_initialized=False,
+        )
+        config_manager.save_config(config)
+
+        console.print(f"[green]Sync configured for project '{name}'[/green]")
+        console.print(f"\nLocal sync path: {resolved_path}")
+        console.print("\nNext steps:")
+        console.print(f"  1. Preview: bm project bisync --name {name} --resync --dry-run")
+        console.print(f"  2. Sync: bm project bisync --name {name} --resync")
+    except Exception as e:
+        console.print(f"[red]Error configuring sync: {str(e)}[/red]")
+        raise typer.Exit(1)
 
 
 @project_app.command("remove")
 def remove_project(
     name: str = typer.Argument(..., help="Name of the project to remove"),
+    delete_notes: bool = typer.Option(
+        False, "--delete-notes", help="Delete project files from disk"
+    ),
 ) -> None:
     """Remove a project."""
 
     async def _remove_project():
         async with get_client() as client:
             project_permalink = generate_permalink(name)
-            response = await call_delete(client, f"/projects/{project_permalink}")
+            response = await call_delete(
+                client, f"/projects/{project_permalink}?delete_notes={delete_notes}"
+            )
             return ProjectStatusResponse.model_validate(response.json())
 
     try:
+        # Get config to check for local sync path and bisync state
+        config = ConfigManager().config
+        local_path = None
+        has_bisync_state = False
+
+        if config.cloud_mode_enabled and name in config.cloud_projects:
+            local_path = config.cloud_projects[name].local_path
+
+            # Check for bisync state
+            from basic_memory.cli.commands.cloud.rclone_commands import get_project_bisync_state
+
+            bisync_state_path = get_project_bisync_state(name)
+            has_bisync_state = bisync_state_path.exists()
+
+        # Remove project from cloud/API
         result = asyncio.run(_remove_project())
         console.print(f"[green]{result.message}[/green]")
+
+        # Clean up local sync directory if it exists and delete_notes is True
+        if delete_notes and local_path:
+            local_dir = Path(local_path)
+            if local_dir.exists():
+                import shutil
+
+                shutil.rmtree(local_dir)
+                console.print(f"[green]Removed local sync directory: {local_path}[/green]")
+
+        # Clean up bisync state if it exists
+        if has_bisync_state:
+            from basic_memory.cli.commands.cloud.rclone_commands import get_project_bisync_state
+            import shutil
+
+            bisync_state_path = get_project_bisync_state(name)
+            if bisync_state_path.exists():
+                shutil.rmtree(bisync_state_path)
+                console.print("[green]Removed bisync state[/green]")
+
+        # Clean up cloud_projects config entry
+        if config.cloud_mode_enabled and name in config.cloud_projects:
+            del config.cloud_projects[name]
+            ConfigManager().save_config(config)
+
+        # Show informative message if files were not deleted
+        if not delete_notes:
+            if local_path:
+                console.print(f"[yellow]Note: Local files remain at {local_path}[/yellow]")
+
     except Exception as e:
         console.print(f"[red]Error removing project: {str(e)}[/red]")
         raise typer.Exit(1)
 
-    # Show this message regardless of method used
-    console.print("[yellow]Note: The project files have not been deleted from disk.[/yellow]")
+
+@project_app.command("default")
+def set_default_project(
+    name: str = typer.Argument(..., help="Name of the project to set as CLI default"),
+) -> None:
+    """Set the default project when 'config.default_project_mode' is set.
+
+    Note: This command is only available in local mode.
+    """
+    config = ConfigManager().config
+
+    if config.cloud_mode_enabled:
+        console.print("[red]Error: 'default' command is not available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    async def _set_default():
+        async with get_client() as client:
+            project_permalink = generate_permalink(name)
+            response = await call_put(client, f"/projects/{project_permalink}/default")
+            return ProjectStatusResponse.model_validate(response.json())
+
+    try:
+        result = asyncio.run(_set_default())
+        console.print(f"[green]{result.message}[/green]")
+    except Exception as e:
+        console.print(f"[red]Error setting default project: {str(e)}[/red]")
+        raise typer.Exit(1)
 
 
-if not config.cloud_mode_enabled:
+@project_app.command("sync-config")
+def synchronize_projects() -> None:
+    """Synchronize project config between configuration file and database.
 
-    @project_app.command("default")
-    def set_default_project(
-        name: str = typer.Argument(..., help="Name of the project to set as CLI default"),
-    ) -> None:
-        """Set the default project when 'config.default_project_mode' is set."""
+    Note: This command is only available in local mode.
+    """
+    config = ConfigManager().config
 
-        async def _set_default():
+    if config.cloud_mode_enabled:
+        console.print("[red]Error: 'sync-config' command is not available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    async def _sync_config():
+        async with get_client() as client:
+            response = await call_post(client, "/projects/config/sync")
+            return ProjectStatusResponse.model_validate(response.json())
+
+    try:
+        result = asyncio.run(_sync_config())
+        console.print(f"[green]{result.message}[/green]")
+    except Exception as e:  # pragma: no cover
+        console.print(f"[red]Error synchronizing projects: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("move")
+def move_project(
+    name: str = typer.Argument(..., help="Name of the project to move"),
+    new_path: str = typer.Argument(..., help="New absolute path for the project"),
+) -> None:
+    """Move a project to a new location.
+
+    Note: This command is only available in local mode.
+    """
+    config = ConfigManager().config
+
+    if config.cloud_mode_enabled:
+        console.print("[red]Error: 'move' command is not available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    # Resolve to absolute path
+    resolved_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
+
+    async def _move_project():
+        async with get_client() as client:
+            data = {"path": resolved_path}
+            project_permalink = generate_permalink(name)
+
+            # TODO fix route to use ProjectPathDep
+            response = await call_patch(client, f"/{name}/project/{project_permalink}", json=data)
+            return ProjectStatusResponse.model_validate(response.json())
+
+    try:
+        result = asyncio.run(_move_project())
+        console.print(f"[green]{result.message}[/green]")
+
+        # Show important file movement reminder
+        console.print()  # Empty line for spacing
+        console.print(
+            Panel(
+                "[bold red]IMPORTANT:[/bold red] Project configuration updated successfully.\n\n"
+                "[yellow]You must manually move your project files from the old location to:[/yellow]\n"
+                f"[cyan]{resolved_path}[/cyan]\n\n"
+                "[dim]Basic Memory has only updated the configuration - your files remain in their original location.[/dim]",
+                title="Manual File Movement Required",
+                border_style="yellow",
+                expand=False,
+            )
+        )
+
+    except Exception as e:
+        console.print(f"[red]Error moving project: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("sync")
+def sync_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to sync"),
+    dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
+) -> None:
+    """One-way sync: local -> cloud (make cloud identical to local).
+
+    Example:
+      bm project sync --name research
+      bm project sync --name research --dry-run
+    """
+    config = ConfigManager().config
+    if not config.cloud_mode_enabled:
+        console.print("[red]Error: sync only available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = asyncio.run(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        async def _get_project():
             async with get_client() as client:
-                project_permalink = generate_permalink(name)
-                response = await call_put(client, f"/projects/{project_permalink}/default")
-                return ProjectStatusResponse.model_validate(response.json())
+                response = await call_get(client, "/projects/projects")
+                projects_list = ProjectList.model_validate(response.json())
+                for proj in projects_list.projects:
+                    if generate_permalink(proj.name) == generate_permalink(name):
+                        return proj
+                return None
 
-        try:
-            result = asyncio.run(_set_default())
-            console.print(f"[green]{result.message}[/green]")
-        except Exception as e:
-            console.print(f"[red]Error setting default project: {str(e)}[/red]")
+        project_data = asyncio.run(_get_project())
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
             raise typer.Exit(1)
 
-    @project_app.command("sync-config")
-    def synchronize_projects() -> None:
-        """Synchronize project config between configuration file and database."""
+        # Get local_sync_path from cloud_projects config
+        local_sync_path = None
+        if name in config.cloud_projects:
+            local_sync_path = config.cloud_projects[name].local_path
 
-        async def _sync_config():
-            async with get_client() as client:
-                response = await call_post(client, "/projects/config/sync")
-                return ProjectStatusResponse.model_validate(response.json())
-
-        try:
-            result = asyncio.run(_sync_config())
-            console.print(f"[green]{result.message}[/green]")
-        except Exception as e:  # pragma: no cover
-            console.print(f"[red]Error synchronizing projects: {str(e)}[/red]")
+        if not local_sync_path:
+            console.print(f"[red]Error: Project '{name}' has no local_sync_path configured[/red]")
+            console.print(f"\nConfigure sync with: bm project sync-setup {name} ~/path/to/local")
             raise typer.Exit(1)
 
-    @project_app.command("move")
-    def move_project(
-        name: str = typer.Argument(..., help="Name of the project to move"),
-        new_path: str = typer.Argument(..., help="New absolute path for the project"),
-    ) -> None:
-        """Move a project to a new location."""
-        # Resolve to absolute path
-        resolved_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
+        # Create SyncProject
+        sync_project = SyncProject(
+            name=project_data.name,
+            path=normalize_project_path(project_data.path),
+            local_sync_path=local_sync_path,
+        )
 
-        async def _move_project():
+        # Run sync
+        console.print(f"[blue]Syncing {name} (local -> cloud)...[/blue]")
+        success = project_sync(sync_project, bucket_name, dry_run=dry_run, verbose=verbose)
+
+        if success:
+            console.print(f"[green]{name} synced successfully[/green]")
+
+            # Trigger database sync if not a dry run
+            if not dry_run:
+
+                async def _trigger_db_sync():
+                    async with get_client() as client:
+                        permalink = generate_permalink(name)
+                        response = await call_post(
+                            client, f"/{permalink}/project/sync?force_full=true", json={}
+                        )
+                        return response.json()
+
+                try:
+                    result = asyncio.run(_trigger_db_sync())
+                    console.print(f"[dim]Database sync initiated: {result.get('message')}[/dim]")
+                except Exception as e:
+                    console.print(f"[yellow]Warning: Could not trigger database sync: {e}[/yellow]")
+        else:
+            console.print(f"[red]{name} sync failed[/red]")
+            raise typer.Exit(1)
+
+    except RcloneError as e:
+        console.print(f"[red]Sync error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("bisync")
+def bisync_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to bisync"),
+    dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
+    resync: bool = typer.Option(False, "--resync", help="Force new baseline"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
+) -> None:
+    """Two-way sync: local <-> cloud (bidirectional sync).
+
+    Examples:
+      bm project bisync --name research --resync  # First time
+      bm project bisync --name research           # Subsequent syncs
+      bm project bisync --name research --dry-run # Preview changes
+    """
+    config = ConfigManager().config
+    if not config.cloud_mode_enabled:
+        console.print("[red]Error: bisync only available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = asyncio.run(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        async def _get_project():
             async with get_client() as client:
-                data = {"path": resolved_path}
-                project_permalink = generate_permalink(name)
+                response = await call_get(client, "/projects/projects")
+                projects_list = ProjectList.model_validate(response.json())
+                for proj in projects_list.projects:
+                    if generate_permalink(proj.name) == generate_permalink(name):
+                        return proj
+                return None
 
-                # TODO fix route to use ProjectPathDep
-                response = await call_patch(
-                    client, f"/{name}/project/{project_permalink}", json=data
-                )
-                return ProjectStatusResponse.model_validate(response.json())
+        project_data = asyncio.run(_get_project())
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
 
-        try:
-            result = asyncio.run(_move_project())
-            console.print(f"[green]{result.message}[/green]")
+        # Get local_sync_path from cloud_projects config
+        local_sync_path = None
+        if name in config.cloud_projects:
+            local_sync_path = config.cloud_projects[name].local_path
 
-            # Show important file movement reminder
-            console.print()  # Empty line for spacing
+        if not local_sync_path:
+            console.print(f"[red]Error: Project '{name}' has no local_sync_path configured[/red]")
+            console.print(f"\nConfigure sync with: bm project sync-setup {name} ~/path/to/local")
+            raise typer.Exit(1)
+
+        # Create SyncProject
+        sync_project = SyncProject(
+            name=project_data.name,
+            path=normalize_project_path(project_data.path),
+            local_sync_path=local_sync_path,
+        )
+
+        # Run bisync
+        console.print(f"[blue]Bisync {name} (local <-> cloud)...[/blue]")
+        success = project_bisync(
+            sync_project, bucket_name, dry_run=dry_run, resync=resync, verbose=verbose
+        )
+
+        if success:
+            console.print(f"[green]{name} bisync completed successfully[/green]")
+
+            # Update config
+            config.cloud_projects[name].last_sync = datetime.now()
+            config.cloud_projects[name].bisync_initialized = True
+            ConfigManager().save_config(config)
+
+            # Trigger database sync if not a dry run
+            if not dry_run:
+
+                async def _trigger_db_sync():
+                    async with get_client() as client:
+                        permalink = generate_permalink(name)
+                        response = await call_post(
+                            client, f"/{permalink}/project/sync?force_full=true", json={}
+                        )
+                        return response.json()
+
+                try:
+                    result = asyncio.run(_trigger_db_sync())
+                    console.print(f"[dim]Database sync initiated: {result.get('message')}[/dim]")
+                except Exception as e:
+                    console.print(f"[yellow]Warning: Could not trigger database sync: {e}[/yellow]")
+        else:
+            console.print(f"[red]{name} bisync failed[/red]")
+            raise typer.Exit(1)
+
+    except RcloneError as e:
+        console.print(f"[red]Bisync error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("check")
+def check_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to check"),
+    one_way: bool = typer.Option(False, "--one-way", help="Check one direction only (faster)"),
+) -> None:
+    """Verify file integrity between local and cloud.
+
+    Example:
+      bm project check --name research
+    """
+    config = ConfigManager().config
+    if not config.cloud_mode_enabled:
+        console.print("[red]Error: check only available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = asyncio.run(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        async def _get_project():
+            async with get_client() as client:
+                response = await call_get(client, "/projects/projects")
+                projects_list = ProjectList.model_validate(response.json())
+                for proj in projects_list.projects:
+                    if generate_permalink(proj.name) == generate_permalink(name):
+                        return proj
+                return None
+
+        project_data = asyncio.run(_get_project())
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
+
+        # Get local_sync_path from cloud_projects config
+        local_sync_path = None
+        if name in config.cloud_projects:
+            local_sync_path = config.cloud_projects[name].local_path
+
+        if not local_sync_path:
+            console.print(f"[red]Error: Project '{name}' has no local_sync_path configured[/red]")
+            console.print(f"\nConfigure sync with: bm project sync-setup {name} ~/path/to/local")
+            raise typer.Exit(1)
+
+        # Create SyncProject
+        sync_project = SyncProject(
+            name=project_data.name,
+            path=normalize_project_path(project_data.path),
+            local_sync_path=local_sync_path,
+        )
+
+        # Run check
+        console.print(f"[blue]Checking {name} integrity...[/blue]")
+        match = project_check(sync_project, bucket_name, one_way=one_way)
+
+        if match:
+            console.print(f"[green]{name} files match[/green]")
+        else:
+            console.print(f"[yellow]!{name} has differences[/yellow]")
+
+    except RcloneError as e:
+        console.print(f"[red]Check error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("bisync-reset")
+def bisync_reset(
+    name: str = typer.Argument(..., help="Project name to reset bisync state for"),
+) -> None:
+    """Clear bisync state for a project.
+
+    This removes the bisync metadata files, forcing a fresh --resync on next bisync.
+    Useful when bisync gets into an inconsistent state or when remote path changes.
+    """
+    from basic_memory.cli.commands.cloud.rclone_commands import get_project_bisync_state
+    import shutil
+
+    try:
+        state_path = get_project_bisync_state(name)
+
+        if not state_path.exists():
+            console.print(f"[yellow]No bisync state found for project '{name}'[/yellow]")
+            return
+
+        # Remove the entire state directory
+        shutil.rmtree(state_path)
+        console.print(f"[green]Cleared bisync state for project '{name}'[/green]")
+        console.print("\nNext steps:")
+        console.print(f"  1. Preview: bm project bisync --name {name} --resync --dry-run")
+        console.print(f"  2. Sync: bm project bisync --name {name} --resync")
+
+    except Exception as e:
+        console.print(f"[red]Error clearing bisync state: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
+@project_app.command("ls")
+def ls_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to list files from"),
+    path: str = typer.Argument(None, help="Path within project (optional)"),
+) -> None:
+    """List files in remote project.
+
+    Examples:
+      bm project ls --name research
+      bm project ls --name research subfolder
+    """
+    config = ConfigManager().config
+    if not config.cloud_mode_enabled:
+        console.print("[red]Error: ls only available in cloud mode[/red]")
+        raise typer.Exit(1)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = asyncio.run(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        async def _get_project():
+            async with get_client() as client:
+                response = await call_get(client, "/projects/projects")
+                projects_list = ProjectList.model_validate(response.json())
+                for proj in projects_list.projects:
+                    if generate_permalink(proj.name) == generate_permalink(name):
+                        return proj
+                return None
+
+        project_data = asyncio.run(_get_project())
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
+
+        # Create SyncProject (local_sync_path not needed for ls)
+        sync_project = SyncProject(
+            name=project_data.name,
+            path=normalize_project_path(project_data.path),
+        )
+
+        # List files
+        files = project_ls(sync_project, bucket_name, path=path)
+
+        if files:
+            console.print(f"\n[bold]Files in {name}" + (f"/{path}" if path else "") + ":[/bold]")
+            for file in files:
+                console.print(f"  {file}")
+            console.print(f"\n[dim]Total: {len(files)} files[/dim]")
+        else:
             console.print(
-                Panel(
-                    "[bold red]IMPORTANT:[/bold red] Project configuration updated successfully.\n\n"
-                    "[yellow]You must manually move your project files from the old location to:[/yellow]\n"
-                    f"[cyan]{resolved_path}[/cyan]\n\n"
-                    "[dim]Basic Memory has only updated the configuration - your files remain in their original location.[/dim]",
-                    title="⚠️  Manual File Movement Required",
-                    border_style="yellow",
-                    expand=False,
-                )
+                f"[yellow]No files found in {name}" + (f"/{path}" if path else "") + "[/yellow]"
             )
 
-        except Exception as e:
-            console.print(f"[red]Error moving project: {str(e)}[/red]")
-            raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
 
 
 @project_app.command("info")
@@ -248,13 +784,13 @@ def display_project_info(
                     f"[bold]Project:[/bold] {info.project_name}\n"
                     f"[bold]Path:[/bold] {info.project_path}\n"
                     f"[bold]Default Project:[/bold] {info.default_project}\n",
-                    title="📊 Basic Memory Project Info",
+                    title="Basic Memory Project Info",
                     expand=False,
                 )
             )
 
             # Statistics section
-            stats_table = Table(title="📈 Statistics")
+            stats_table = Table(title="Statistics")
             stats_table.add_column("Metric", style="cyan")
             stats_table.add_column("Count", style="green")
 
@@ -270,7 +806,7 @@ def display_project_info(
 
             # Entity types
             if info.statistics.entity_types:
-                entity_types_table = Table(title="📑 Entity Types")
+                entity_types_table = Table(title="Entity Types")
                 entity_types_table.add_column("Type", style="blue")
                 entity_types_table.add_column("Count", style="green")
 
@@ -281,7 +817,7 @@ def display_project_info(
 
             # Most connected entities
             if info.statistics.most_connected_entities:  # pragma: no cover
-                connected_table = Table(title="🔗 Most Connected Entities")
+                connected_table = Table(title="Most Connected Entities")
                 connected_table.add_column("Title", style="blue")
                 connected_table.add_column("Permalink", style="cyan")
                 connected_table.add_column("Relations", style="green")
@@ -295,7 +831,7 @@ def display_project_info(
 
             # Recent activity
             if info.activity.recently_updated:  # pragma: no cover
-                recent_table = Table(title="🕒 Recent Activity")
+                recent_table = Table(title="Recent Activity")
                 recent_table.add_column("Title", style="blue")
                 recent_table.add_column("Type", style="cyan")
                 recent_table.add_column("Last Updated", style="green")
@@ -315,7 +851,7 @@ def display_project_info(
                 console.print(recent_table)
 
             # Available projects
-            projects_table = Table(title="📁 Available Projects")
+            projects_table = Table(title="Available Projects")
             projects_table.add_column("Name", style="blue")
             projects_table.add_column("Path", style="cyan")
             projects_table.add_column("Default", style="green")
@@ -323,7 +859,7 @@ def display_project_info(
             for name, proj_info in info.available_projects.items():
                 is_default = name == info.default_project
                 project_path = proj_info["path"]
-                projects_table.add_row(name, project_path, "✓" if is_default else "")
+                projects_table.add_row(name, project_path, "[X]" if is_default else "")
 
             console.print(projects_table)
 

src/basic_memory/cli/commands/status.py

@@ -94,7 +94,7 @@ def display_changes(
     """Display changes using Rich for better visualization."""
     tree = Tree(f"{project_name}: {title}")
 
-    if changes.total == 0:
+    if changes.total == 0 and not changes.skipped_files:
         tree.add("No changes")
         console.print(Panel(tree, expand=False))
         return
@@ -114,6 +114,13 @@ def display_changes(
         if changes.deleted:
             del_branch = tree.add("[red]Deleted[/red]")
             add_files_to_tree(del_branch, changes.deleted, "red")
+        if changes.skipped_files:
+            skip_branch = tree.add("[red]! Skipped (Circuit Breaker)[/red]")
+            for skipped in sorted(changes.skipped_files, key=lambda x: x.path):
+                skip_branch.add(
+                    f"[red]{skipped.path}[/red] "
+                    f"(failures: {skipped.failure_count}, reason: {skipped.reason})"
+                )
     else:
         # Show directory summaries
         by_dir = group_changes_by_directory(changes)
@@ -122,6 +129,14 @@ def display_changes(
             if summary:  # Only show directories with changes
                 tree.add(f"[bold]{dir_name}/[/bold] {summary}")
 
+        # Show skipped files summary in non-verbose mode
+        if changes.skipped_files:
+            skip_count = len(changes.skipped_files)
+            tree.add(
+                f"[red]! {skip_count} file{'s' if skip_count != 1 else ''} "
+                f"skipped due to repeated failures[/red]"
+            )
+
     console.print(Panel(tree, expand=False))
 
 
@@ -137,7 +152,7 @@ async def run_status(project: Optional[str] = None, verbose: bool = False):  # p
             display_changes(project_item.name, "Status", sync_report, verbose)
 
     except (ValueError, ToolError) as e:
-        console.print(f"[red]✗ Error: {e}[/red]")
+        console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(1)
 
 

src/basic_memory/cli/commands/sync.py

@@ -1,59 +0,0 @@
-"""Command module for basic-memory sync operations."""
-
-import asyncio
-from typing import Annotated, Optional
-
-import typer
-
-from basic_memory.cli.app import app
-from basic_memory.cli.commands.command_utils import run_sync
-from basic_memory.config import ConfigManager
-
-
-@app.command()
-def sync(
-    project: Annotated[
-        Optional[str],
-        typer.Option(help="The project name."),
-    ] = None,
-    watch: Annotated[
-        bool,
-        typer.Option("--watch", help="Run continuous sync (cloud mode only)"),
-    ] = False,
-    interval: Annotated[
-        int,
-        typer.Option("--interval", help="Sync interval in seconds for watch mode (default: 60)"),
-    ] = 60,
-) -> None:
-    """Sync knowledge files with the database.
-
-    In local mode: Scans filesystem and updates database.
-    In cloud mode: Runs bidirectional file sync (bisync) then updates database.
-
-    Examples:
-      bm sync                    # One-time sync
-      bm sync --watch            # Continuous sync every 60s
-      bm sync --watch --interval 30  # Continuous sync every 30s
-    """
-    config = ConfigManager().config
-
-    if config.cloud_mode_enabled:
-        # Cloud mode: run bisync which includes database sync
-        from basic_memory.cli.commands.cloud.bisync_commands import run_bisync, run_bisync_watch
-
-        try:
-            if watch:
-                run_bisync_watch(interval_seconds=interval)
-            else:
-                run_bisync()
-        except Exception:
-            raise typer.Exit(1)
-    else:
-        # Local mode: just database sync
-        if watch:
-            typer.echo(
-                "Error: --watch is only available in cloud mode. Run 'bm cloud login' first."
-            )
-            raise typer.Exit(1)
-
-        asyncio.run(run_sync(project))

src/basic_memory/cli/main.py

@@ -13,7 +13,6 @@ from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
     mcp,
     project,
     status,
-    sync,
     tool,
 )
 

src/basic_memory/config.py

@@ -3,11 +3,13 @@
 import json
 import os
 from dataclasses import dataclass
+from datetime import datetime
 from pathlib import Path
 from typing import Any, Dict, Literal, Optional, List, Tuple
+from enum import Enum
 
 from loguru import logger
-from pydantic import Field, field_validator
+from pydantic import BaseModel, Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 import basic_memory
@@ -23,6 +25,13 @@ WATCH_STATUS_JSON = "watch-status.json"
 Environment = Literal["test", "dev", "user"]
 
 
+class DatabaseBackend(str, Enum):
+    """Supported database backends."""
+
+    SQLITE = "sqlite"
+    POSTGRES = "postgres"
+
+
 @dataclass
 class ProjectConfig:
     """Configuration for a specific basic-memory project."""
@@ -39,6 +48,22 @@ class ProjectConfig:
         return f"/{generate_permalink(self.name)}"
 
 
+class CloudProjectConfig(BaseModel):
+    """Sync configuration for a cloud project.
+
+    This tracks the local working directory and sync state for a project
+    that is synced with Basic Memory Cloud.
+    """
+
+    local_path: str = Field(description="Local working directory path for this cloud project")
+    last_sync: Optional[datetime] = Field(
+        default=None, description="Timestamp of last successful sync operation"
+    )
+    bisync_initialized: bool = Field(
+        default=False, description="Whether rclone bisync baseline has been established"
+    )
+
+
 class BasicMemoryConfig(BaseSettings):
     """Pydantic model for Basic Memory global configuration."""
 
@@ -46,8 +71,10 @@ class BasicMemoryConfig(BaseSettings):
 
     projects: Dict[str, str] = Field(
         default_factory=lambda: {
-            "main": Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")).as_posix()
-        },
+            "main": str(Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")))
+        }
+        if os.getenv("BASIC_MEMORY_HOME")
+        else {},
         description="Mapping of project names to their filesystem paths",
     )
     default_project: str = Field(
@@ -62,6 +89,17 @@ class BasicMemoryConfig(BaseSettings):
     # overridden by ~/.basic-memory/config.json
     log_level: str = "INFO"
 
+    # Database configuration
+    database_backend: DatabaseBackend = Field(
+        default=DatabaseBackend.SQLITE,
+        description="Database backend to use (sqlite or postgres)",
+    )
+
+    database_url: Optional[str] = Field(
+        default=None,
+        description="Database connection URL. For Postgres, use postgresql+asyncpg://user:pass@host:port/db. If not set, SQLite will use default path.",
+    )
+
     # Watch service configuration
     sync_delay: int = Field(
         default=1000, description="Milliseconds to wait after changes before syncing", gt=0
@@ -84,7 +122,19 @@ class BasicMemoryConfig(BaseSettings):
 
     sync_thread_pool_size: int = Field(
         default=4,
-        description="Size of thread pool for file I/O operations in sync service",
+        description="Size of thread pool for file I/O operations in sync service. Default of 4 is optimized for cloud deployments with 1-2GB RAM.",
+        gt=0,
+    )
+
+    sync_max_concurrent_files: int = Field(
+        default=10,
+        description="Maximum number of files to process concurrently during sync. Limits memory usage on large projects (2000+ files). Lower values reduce memory consumption.",
+        gt=0,
+    )
+
+    sync_batch_size: int = Field(
+        default=100,
+        description="Number of files to process in a single database transaction during sync. Higher values improve performance with remote databases (Postgres) but increase memory usage. Typical values: 100 (conservative), 500 (balanced), 1000 (aggressive).",
         gt=0,
     )
 
@@ -132,6 +182,11 @@ class BasicMemoryConfig(BaseSettings):
         description="Enable cloud mode - all requests go to cloud instead of local (config file value)",
     )
 
+    cloud_projects: Dict[str, CloudProjectConfig] = Field(
+        default_factory=dict,
+        description="Cloud project sync configuration mapping project names to their local paths and sync state",
+    )
+
     @property
     def cloud_mode_enabled(self) -> bool:
         """Check if cloud mode is enabled.
@@ -148,14 +203,6 @@ class BasicMemoryConfig(BaseSettings):
         # Fall back to config file value
         return self.cloud_mode
 
-    bisync_config: Dict[str, Any] = Field(
-        default_factory=lambda: {
-            "profile": "balanced",
-            "sync_dir": str(Path.home() / "basic-memory-cloud-sync"),
-        },
-        description="Bisync configuration for cloud sync",
-    )
-
     model_config = SettingsConfigDict(
         env_prefix="BASIC_MEMORY_",
         extra="ignore",
@@ -172,15 +219,16 @@ class BasicMemoryConfig(BaseSettings):
 
     def model_post_init(self, __context: Any) -> None:
         """Ensure configuration is valid after initialization."""
-        # Ensure main project exists
-        if "main" not in self.projects:  # pragma: no cover
-            self.projects["main"] = (
+        # Ensure at least one project exists; if none exist then create main
+        if not self.projects:  # pragma: no cover
+            self.projects["main"] = str(
                 Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory"))
-            ).as_posix()
+            )
 
-        # Ensure default project is valid
+        # Ensure default project is valid (i.e. points to an existing project)
         if self.default_project not in self.projects:  # pragma: no cover
-            self.default_project = "main"
+            # Set default to first available project
+            self.default_project = next(iter(self.projects.keys()))
 
     @property
     def app_database_path(self) -> Path:
@@ -338,7 +386,7 @@ class ConfigManager:
 
         # Load config, modify it, and save it
         config = self.load_config()
-        config.projects[name] = project_path.as_posix()
+        config.projects[name] = str(project_path)
         self.save_config(config)
         return ProjectConfig(name=name, home=project_path)
 
@@ -421,7 +469,9 @@ def get_project_config(project_name: Optional[str] = None) -> ProjectConfig:
 def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None:
     """Save configuration to file."""
     try:
-        file_path.write_text(json.dumps(config.model_dump(), indent=2))
+        # Use model_dump with mode='json' to serialize datetime objects properly
+        config_dict = config.model_dump(mode="json")
+        file_path.write_text(json.dumps(config_dict, indent=2))
     except Exception as e:  # pragma: no cover
         logger.error(f"Failed to save config: {e}")
 

src/basic_memory/db.py

@@ -5,7 +5,7 @@ from enum import Enum, auto
 from pathlib import Path
 from typing import AsyncGenerator, Optional
 
-from basic_memory.config import BasicMemoryConfig, ConfigManager
+from basic_memory.config import BasicMemoryConfig, ConfigManager, DatabaseBackend
 from alembic import command
 from alembic.config import Config
 
@@ -20,12 +20,12 @@ from sqlalchemy.ext.asyncio import (
 )
 from sqlalchemy.pool import NullPool
 
-from basic_memory.repository.search_repository import SearchRepository
+from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
+from basic_memory.repository.sqlite_search_repository import SQLiteSearchRepository
 
 # Module level state
 _engine: Optional[AsyncEngine] = None
 _session_maker: Optional[async_sessionmaker[AsyncSession]] = None
-_migrations_completed: bool = False
 
 
 class DatabaseType(Enum):
@@ -35,8 +35,33 @@ class DatabaseType(Enum):
     FILESYSTEM = auto()
 
     @classmethod
-    def get_db_url(cls, db_path: Path, db_type: "DatabaseType") -> str:
-        """Get SQLAlchemy URL for database path."""
+    def get_db_url(
+        cls, db_path: Path, db_type: "DatabaseType", config: Optional[BasicMemoryConfig] = None
+    ) -> str:
+        """Get SQLAlchemy URL for database path.
+
+        Args:
+            db_path: Path to SQLite database file (ignored for Postgres)
+            db_type: Type of database (MEMORY or FILESYSTEM)
+            config: Optional config to check for database backend and URL
+
+        Returns:
+            SQLAlchemy connection URL
+        """
+        # Load config if not provided
+        if config is None:
+            config = ConfigManager().config
+
+        # Check if Postgres backend is configured
+        if config.database_backend == DatabaseBackend.POSTGRES:
+            if not config.database_url:
+                raise ValueError("DATABASE_URL must be set when using Postgres backend")
+            logger.info(
+                f"Using Postgres database: {config.database_url.split('@')[1] if '@' in config.database_url else config.database_url}"
+            )
+            return config.database_url
+
+        # Default to SQLite
         if db_type == cls.MEMORY:
             logger.info("Using in-memory SQLite database")
             return "sqlite+aiosqlite://"
@@ -64,7 +89,14 @@ async def scoped_session(
     factory = get_scoped_session_factory(session_maker)
     session = factory()
     try:
-        await session.execute(text("PRAGMA foreign_keys=ON"))
+        # Only enable foreign keys for SQLite (Postgres has them enabled by default)
+        # Detect database type from session's bind (engine) dialect
+        engine = session.get_bind()
+        dialect_name = engine.dialect.name
+
+        if dialect_name == "sqlite":
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+
         yield session
         await session.commit()
     except Exception:
@@ -103,13 +135,16 @@ def _configure_sqlite_connection(dbapi_conn, enable_wal: bool = True) -> None:
         cursor.close()
 
 
-def _create_engine_and_session(
-    db_path: Path, db_type: DatabaseType = DatabaseType.FILESYSTEM
-) -> tuple[AsyncEngine, async_sessionmaker[AsyncSession]]:
-    """Internal helper to create engine and session maker."""
-    db_url = DatabaseType.get_db_url(db_path, db_type)
-    logger.debug(f"Creating engine for db_url: {db_url}")
+def _create_sqlite_engine(db_url: str, db_type: DatabaseType) -> AsyncEngine:
+    """Create SQLite async engine with appropriate configuration.
 
+    Args:
+        db_url: SQLite connection URL
+        db_type: Database type (MEMORY or FILESYSTEM)
+
+    Returns:
+        Configured async engine for SQLite
+    """
     # Configure connection args with Windows-specific settings
     connect_args: dict[str, bool | float | None] = {"check_same_thread": False}
 
@@ -146,6 +181,50 @@ def _create_engine_and_session(
         """Enable WAL mode on each connection."""
         _configure_sqlite_connection(dbapi_conn, enable_wal=enable_wal)
 
+    return engine
+
+
+def _create_postgres_engine(db_url: str) -> AsyncEngine:
+    """Create Postgres async engine with appropriate configuration.
+
+    Args:
+        db_url: Postgres connection URL (postgresql+asyncpg://...)
+
+    Returns:
+        Configured async engine for Postgres
+    """
+    # Postgres with asyncpg - use standard async connection
+    engine = create_async_engine(
+        db_url,
+        echo=False,
+        pool_pre_ping=True,  # Verify connections before using them
+    )
+
+    return engine
+
+
+def _create_engine_and_session(
+    db_path: Path, db_type: DatabaseType = DatabaseType.FILESYSTEM
+) -> tuple[AsyncEngine, async_sessionmaker[AsyncSession]]:
+    """Internal helper to create engine and session maker.
+
+    Args:
+        db_path: Path to database file (used for SQLite, ignored for Postgres)
+        db_type: Type of database (MEMORY or FILESYSTEM)
+
+    Returns:
+        Tuple of (engine, session_maker)
+    """
+    config = ConfigManager().config
+    db_url = DatabaseType.get_db_url(db_path, db_type, config)
+    logger.debug(f"Creating engine for db_url: {db_url}")
+
+    # Delegate to backend-specific engine creation
+    if config.database_backend == DatabaseBackend.POSTGRES:
+        engine = _create_postgres_engine(db_url)
+    else:
+        engine = _create_sqlite_engine(db_url, db_type)
+
     session_maker = async_sessionmaker(engine, expire_on_commit=False)
     return engine, session_maker
 
@@ -181,13 +260,12 @@ async def get_or_create_db(
 
 async def shutdown_db() -> None:  # pragma: no cover
     """Clean up database connections."""
-    global _engine, _session_maker, _migrations_completed
+    global _engine, _session_maker
 
     if _engine:
         await _engine.dispose()
         _engine = None
         _session_maker = None
-        _migrations_completed = False
 
 
 @asynccontextmanager
@@ -201,50 +279,12 @@ async def engine_session_factory(
     for each test. For production use, use get_or_create_db() instead.
     """
 
-    global _engine, _session_maker, _migrations_completed
+    global _engine, _session_maker
 
-    db_url = DatabaseType.get_db_url(db_path, db_type)
-    logger.debug(f"Creating engine for db_url: {db_url}")
-
-    # Configure connection args with Windows-specific settings
-    connect_args: dict[str, bool | float | None] = {"check_same_thread": False}
-
-    # Add Windows-specific parameters to improve reliability
-    if os.name == "nt":  # Windows
-        connect_args.update(
-            {
-                "timeout": 30.0,  # Increase timeout to 30 seconds for Windows
-                "isolation_level": None,  # Use autocommit mode
-            }
-        )
-        # Use NullPool for Windows filesystem databases to avoid connection pooling issues
-        # Important: Do NOT use NullPool for in-memory databases as it will destroy the database
-        # between connections
-        if db_type == DatabaseType.FILESYSTEM:
-            _engine = create_async_engine(
-                db_url,
-                connect_args=connect_args,
-                poolclass=NullPool,  # Disable connection pooling on Windows
-                echo=False,
-            )
-        else:
-            # In-memory databases need connection pooling to maintain state
-            _engine = create_async_engine(db_url, connect_args=connect_args)
-    else:
-        _engine = create_async_engine(db_url, connect_args=connect_args)
-
-    # Enable WAL mode for better concurrency and reliability
-    # Note: WAL mode is not supported for in-memory databases
-    enable_wal = db_type != DatabaseType.MEMORY
-
-    @event.listens_for(_engine.sync_engine, "connect")
-    def enable_wal_mode(dbapi_conn, connection_record):
-        """Enable WAL mode on each connection."""
-        _configure_sqlite_connection(dbapi_conn, enable_wal=enable_wal)
+    # Use the same helper function as production code
+    _engine, _session_maker = _create_engine_and_session(db_path, db_type)
 
     try:
-        _session_maker = async_sessionmaker(_engine, expire_on_commit=False)
-
         # Verify that engine and session maker are initialized
         if _engine is None:  # pragma: no cover
             logger.error("Database engine is None in engine_session_factory")
@@ -260,20 +300,16 @@ async def engine_session_factory(
             await _engine.dispose()
             _engine = None
             _session_maker = None
-            _migrations_completed = False
 
 
 async def run_migrations(
-    app_config: BasicMemoryConfig, database_type=DatabaseType.FILESYSTEM, force: bool = False
+    app_config: BasicMemoryConfig, database_type=DatabaseType.FILESYSTEM
 ):  # pragma: no cover
-    """Run any pending alembic migrations."""
-    global _migrations_completed
-
-    # Skip if migrations already completed unless forced
-    if _migrations_completed and not force:
-        logger.debug("Migrations already completed in this session, skipping")
-        return
+    """Run any pending alembic migrations.
 
+    Note: Alembic tracks which migrations have been applied via the alembic_version table,
+    so it's safe to call this multiple times - it will only run pending migrations.
+    """
     logger.info("Running database migrations...")
     try:
         # Get the absolute path to the alembic directory relative to this file
@@ -288,9 +324,16 @@ async def run_migrations(
         )
         config.set_main_option("timezone", "UTC")
         config.set_main_option("revision_environment", "false")
-        config.set_main_option(
-            "sqlalchemy.url", DatabaseType.get_db_url(app_config.database_path, database_type)
-        )
+
+        # Get the correct database URL based on backend configuration
+        db_url = DatabaseType.get_db_url(app_config.database_path, database_type, app_config)
+
+        # For Postgres, Alembic needs synchronous driver (psycopg2), not async (asyncpg)
+        if app_config.database_backend == DatabaseBackend.POSTGRES:
+            # Convert asyncpg URL to psycopg2 URL for Alembic
+            db_url = db_url.replace("postgresql+asyncpg://", "postgresql://")
+
+        config.set_main_option("sqlalchemy.url", db_url)
 
         command.upgrade(config, "head")
         logger.info("Migrations completed successfully")
@@ -301,12 +344,14 @@ async def run_migrations(
         else:
             session_maker = _session_maker
 
-        # initialize the search Index schema
-        # the project_id is not used for init_search_index, so we pass a dummy value
-        await SearchRepository(session_maker, 1).init_search_index()
-
-        # Mark migrations as completed
-        _migrations_completed = True
+        # Initialize the search index schema
+        # For SQLite: Create FTS5 virtual table
+        # For Postgres: No-op (tsvector column added by migrations)
+        # The project_id is not used for init_search_index, so we pass a dummy value
+        if app_config.database_backend == DatabaseBackend.POSTGRES:
+            await PostgresSearchRepository(session_maker, 1).init_search_index()
+        else:
+            await SQLiteSearchRepository(session_maker, 1).init_search_index()
     except Exception as e:  # pragma: no cover
         logger.error(f"Error running migrations: {e}")
         raise

src/basic_memory/deps.py

@@ -25,7 +25,7 @@ from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.repository.observation_repository import ObservationRepository
 from basic_memory.repository.project_repository import ProjectRepository
 from basic_memory.repository.relation_repository import RelationRepository
-from basic_memory.repository.search_repository import SearchRepository
+from basic_memory.repository.search_repository import SearchRepository, create_search_repository
 from basic_memory.services import EntityService, ProjectService
 from basic_memory.services.context_service import ContextService
 from basic_memory.services.directory_service import DirectoryService
@@ -214,8 +214,12 @@ async def get_search_repository(
     session_maker: SessionMakerDep,
     project_id: ProjectIdDep,
 ) -> SearchRepository:
-    """Create a SearchRepository instance for the current project."""
-    return SearchRepository(session_maker, project_id=project_id)
+    """Create a backend-specific SearchRepository instance for the current project.
+
+    Uses factory function to return SQLiteSearchRepository or PostgresSearchRepository
+    based on database backend configuration.
+    """
+    return create_search_repository(session_maker, project_id=project_id)
 
 
 SearchRepositoryDep = Annotated[SearchRepository, Depends(get_search_repository)]
@@ -321,6 +325,7 @@ async def get_sync_service(
     entity_parser: EntityParserDep,
     entity_repository: EntityRepositoryDep,
     relation_repository: RelationRepositoryDep,
+    project_repository: ProjectRepositoryDep,
     search_service: SearchServiceDep,
     file_service: FileServiceDep,
 ) -> SyncService:  # pragma: no cover
@@ -334,6 +339,7 @@ async def get_sync_service(
         entity_parser=entity_parser,
         entity_repository=entity_repository,
         relation_repository=relation_repository,
+        project_repository=project_repository,
         search_service=search_service,
         file_service=file_service,
     )

src/basic_memory/file_utils.py

@@ -5,6 +5,7 @@ from pathlib import Path
 import re
 from typing import Any, Dict, Union
 
+import aiofiles
 import yaml
 import frontmatter
 from loguru import logger
@@ -52,29 +53,12 @@ async def compute_checksum(content: Union[str, bytes]) -> str:
         raise FileError(f"Failed to compute checksum: {e}")
 
 
-async def ensure_directory(path: FilePath) -> None:
-    """
-    Ensure directory exists, creating if necessary.
-
-    Args:
-        path: Directory path to ensure (Path or string)
-
-    Raises:
-        FileWriteError: If directory creation fails
-    """
-    try:
-        # Convert string to Path if needed
-        path_obj = Path(path) if isinstance(path, str) else path
-        path_obj.mkdir(parents=True, exist_ok=True)
-    except Exception as e:  # pragma: no cover
-        logger.error("Failed to create directory", path=str(path), error=str(e))
-        raise FileWriteError(f"Failed to create directory {path}: {e}")
-
-
 async def write_file_atomic(path: FilePath, content: str) -> None:
     """
     Write file with atomic operation using temporary file.
 
+    Uses aiofiles for true async I/O (non-blocking).
+
     Args:
         path: Target file path (Path or string)
         content: Content to write
@@ -87,7 +71,11 @@ async def write_file_atomic(path: FilePath, content: str) -> None:
     temp_path = path_obj.with_suffix(".tmp")
 
     try:
-        temp_path.write_text(content, encoding="utf-8")
+        # Use aiofiles for non-blocking write
+        async with aiofiles.open(temp_path, mode="w", encoding="utf-8") as f:
+            await f.write(content)
+
+        # Atomic rename (this is fast, doesn't need async)
         temp_path.replace(path_obj)
         logger.debug("Wrote file atomically", path=str(path_obj), content_length=len(content))
     except Exception as e:  # pragma: no cover
@@ -185,74 +173,26 @@ def remove_frontmatter(content: str) -> str:
     return parts[2].strip()
 
 
-async def update_frontmatter(path: FilePath, updates: Dict[str, Any]) -> str:
-    """Update frontmatter fields in a file while preserving all content.
-
-    Only modifies the frontmatter section, leaving all content untouched.
-    Creates frontmatter section if none exists.
-    Returns checksum of updated file.
-
-    Args:
-        path: Path to markdown file (Path or string)
-        updates: Dict of frontmatter fields to update
-
-    Returns:
-        Checksum of updated file
-
-    Raises:
-        FileError: If file operations fail
-        ParseError: If frontmatter parsing fails
-    """
-    try:
-        # Convert string to Path if needed
-        path_obj = Path(path) if isinstance(path, str) else path
-
-        # Read current content
-        content = path_obj.read_text(encoding="utf-8")
-
-        # Parse current frontmatter
-        current_fm = {}
-        if has_frontmatter(content):
-            current_fm = parse_frontmatter(content)
-            content = remove_frontmatter(content)
-
-        # Update frontmatter
-        new_fm = {**current_fm, **updates}
-
-        # Write new file with updated frontmatter
-        yaml_fm = yaml.dump(new_fm, sort_keys=False, allow_unicode=True)
-        final_content = f"---\n{yaml_fm}---\n\n{content.strip()}"
-
-        logger.debug("Updating frontmatter", path=str(path_obj), update_keys=list(updates.keys()))
-
-        await write_file_atomic(path_obj, final_content)
-        return await compute_checksum(final_content)
-
-    except Exception as e:  # pragma: no cover
-        logger.error(
-            "Failed to update frontmatter",
-            path=str(path) if isinstance(path, (str, Path)) else "<unknown>",
-            error=str(e),
-        )
-        raise FileError(f"Failed to update frontmatter: {e}")
-
-
 def dump_frontmatter(post: frontmatter.Post) -> str:
     """
     Serialize frontmatter.Post to markdown with Obsidian-compatible YAML format.
 
-    This function ensures that tags are formatted as YAML lists instead of JSON arrays:
+    This function ensures that:
+    1. Tags are formatted as YAML lists instead of JSON arrays
+    2. String values are properly quoted to handle special characters (colons, etc.)
 
     Good (Obsidian compatible):
     ---
+    title: "L2 Governance Core (Split: Core)"
     tags:
     - system
     - overview
     - reference
     ---
 
-    Bad (current behavior):
+    Bad (causes parsing errors):
     ---
+    title: L2 Governance Core (Split: Core)  # Unquoted colon breaks YAML
     tags: ["system", "overview", "reference"]
     ---
 
@@ -267,8 +207,13 @@ def dump_frontmatter(post: frontmatter.Post) -> str:
         return post.content
 
     # Serialize YAML with block style for lists
+    # SafeDumper automatically quotes values with special characters (colons, etc.)
     yaml_str = yaml.dump(
-        post.metadata, sort_keys=False, allow_unicode=True, default_flow_style=False
+        post.metadata,
+        sort_keys=False,
+        allow_unicode=True,
+        default_flow_style=False,
+        Dumper=yaml.SafeDumper,
     )
 
     # Construct the final markdown with frontmatter

src/basic_memory/ignore_utils.py

@@ -172,15 +172,16 @@ def load_bmignore_patterns() -> Set[str]:
     return patterns
 
 
-def load_gitignore_patterns(base_path: Path) -> Set[str]:
+def load_gitignore_patterns(base_path: Path, use_gitignore: bool = True) -> Set[str]:
     """Load gitignore patterns from .gitignore file and .bmignore.
 
     Combines patterns from:
     1. ~/.basic-memory/.bmignore (user's global ignore patterns)
-    2. {base_path}/.gitignore (project-specific patterns)
+    2. {base_path}/.gitignore (project-specific patterns, if use_gitignore=True)
 
     Args:
         base_path: The base directory to search for .gitignore file
+        use_gitignore: If False, only load patterns from .bmignore (default: True)
 
     Returns:
         Set of patterns to ignore
@@ -188,18 +189,19 @@ def load_gitignore_patterns(base_path: Path) -> Set[str]:
     # Start with patterns from .bmignore
     patterns = load_bmignore_patterns()
 
-    gitignore_file = base_path / ".gitignore"
-    if gitignore_file.exists():
-        try:
-            with gitignore_file.open("r", encoding="utf-8") as f:
-                for line in f:
-                    line = line.strip()
-                    # Skip empty lines and comments
-                    if line and not line.startswith("#"):
-                        patterns.add(line)
-        except Exception:
-            # If we can't read .gitignore, just use default patterns
-            pass
+    if use_gitignore:
+        gitignore_file = base_path / ".gitignore"
+        if gitignore_file.exists():
+            try:
+                with gitignore_file.open("r", encoding="utf-8") as f:
+                    for line in f:
+                        line = line.strip()
+                        # Skip empty lines and comments
+                        if line and not line.startswith("#"):
+                            patterns.add(line)
+            except Exception:
+                # If we can't read .gitignore, just use default patterns
+                pass
 
     return patterns
 

src/basic_memory/importers/claude_conversations_importer.py

@@ -153,7 +153,12 @@ class ClaudeConversationsImporter(Importer[ChatImportResult]):
             # Handle message content
             content = msg.get("text", "")
             if msg.get("content"):
-                content = " ".join(c.get("text", "") for c in msg["content"])
+                # Filter out None values before joining
+                content = " ".join(
+                    str(c.get("text", ""))
+                    for c in msg["content"]
+                    if c and c.get("text") is not None
+                )
             lines.append(content)
 
             # Handle attachments

src/basic_memory/markdown/entity_parser.py

@@ -4,12 +4,14 @@ Uses markdown-it with plugins to parse structured data from markdown content.
 """
 
 from dataclasses import dataclass, field
-from datetime import datetime
+from datetime import date, datetime
 from pathlib import Path
 from typing import Any, Optional
 
 import dateparser
 import frontmatter
+import yaml
+from loguru import logger
 from markdown_it import MarkdownIt
 
 from basic_memory.markdown.plugins import observation_plugin, relation_plugin
@@ -24,6 +26,82 @@ from basic_memory.utils import parse_tags
 md = MarkdownIt().use(observation_plugin).use(relation_plugin)
 
 
+def normalize_frontmatter_value(value: Any) -> Any:
+    """Normalize frontmatter values to safe types for processing.
+
+    PyYAML automatically converts various string-like values into native Python types:
+    - Date strings ("2025-10-24") → datetime.date objects
+    - Numbers ("1.0") → int or float
+    - Booleans ("true") → bool
+    - Lists → list objects
+
+    This can cause AttributeError when code expects strings and calls string methods
+    like .strip() on these values (see GitHub issue #236).
+
+    This function normalizes all frontmatter values to safe types:
+    - Dates/datetimes → ISO format strings
+    - Numbers (int/float) → strings
+    - Booleans → strings ("True"/"False")
+    - Lists → preserved as lists, but items are recursively normalized
+    - Dicts → preserved as dicts, but values are recursively normalized
+    - Strings → kept as-is
+    - None → kept as None
+
+    Args:
+        value: The frontmatter value to normalize
+
+    Returns:
+        The normalized value safe for string operations
+
+    Example:
+        >>> normalize_frontmatter_value(datetime.date(2025, 10, 24))
+        '2025-10-24'
+        >>> normalize_frontmatter_value([datetime.date(2025, 10, 24), "tag", 123])
+        ['2025-10-24', 'tag', '123']
+        >>> normalize_frontmatter_value(True)
+        'True'
+    """
+    # Convert date/datetime objects to ISO format strings
+    if isinstance(value, datetime):
+        return value.isoformat()
+    if isinstance(value, date):
+        return value.isoformat()
+
+    # Convert boolean to string (must come before int check since bool is subclass of int)
+    if isinstance(value, bool):
+        return str(value)
+
+    # Convert numbers to strings
+    if isinstance(value, (int, float)):
+        return str(value)
+
+    # Recursively process lists (preserve as list, normalize items)
+    if isinstance(value, list):
+        return [normalize_frontmatter_value(item) for item in value]
+
+    # Recursively process dicts (preserve as dict, normalize values)
+    if isinstance(value, dict):
+        return {key: normalize_frontmatter_value(val) for key, val in value.items()}
+
+    # Keep strings and None as-is
+    return value
+
+
+def normalize_frontmatter_metadata(metadata: dict) -> dict:
+    """Normalize all values in frontmatter metadata dict.
+
+    Converts date/datetime objects to ISO format strings to prevent
+    AttributeError when code expects strings (GitHub issue #236).
+
+    Args:
+        metadata: The frontmatter metadata dictionary
+
+    Returns:
+        A new dictionary with all values normalized
+    """
+    return {key: normalize_frontmatter_value(value) for key, value in metadata.items()}
+
+
 @dataclass
 class EntityContent:
     content: str
@@ -111,18 +189,45 @@ class EntityParser:
         return self.base_path / path
 
     async def parse_file_content(self, absolute_path, file_content):
-        post = frontmatter.loads(file_content)
+        # Parse frontmatter with proper error handling for malformed YAML (issue #185)
+        try:
+            post = frontmatter.loads(file_content)
+        except yaml.YAMLError as e:
+            # Log the YAML parsing error with file context
+            logger.warning(
+                f"Failed to parse YAML frontmatter in {absolute_path}: {e}. "
+                f"Treating file as plain markdown without frontmatter."
+            )
+            # Create a post with no frontmatter - treat entire content as markdown
+            post = frontmatter.Post(file_content, metadata={})
+
         # Extract file stat info
         file_stats = absolute_path.stat()
-        metadata = post.metadata
-        metadata["title"] = post.metadata.get("title", absolute_path.stem)
-        metadata["type"] = post.metadata.get("type", "note")
-        tags = parse_tags(post.metadata.get("tags", []))  # pyright: ignore
+
+        # Normalize frontmatter values to prevent AttributeError on date objects (issue #236)
+        # PyYAML automatically converts date strings like "2025-10-24" to datetime.date objects
+        # This normalization converts them back to ISO format strings to ensure compatibility
+        # with code that expects string values
+        metadata = normalize_frontmatter_metadata(post.metadata)
+
+        # Ensure required fields have defaults (issue #184, #387)
+        # Handle title - use default if missing, None/null, empty, or string "None"
+        title = metadata.get("title")
+        if not title or title == "None":
+            metadata["title"] = absolute_path.stem
+        else:
+            metadata["title"] = title
+        # Handle type - use default if missing OR explicitly set to None/null
+        entity_type = metadata.get("type")
+        metadata["type"] = entity_type if entity_type is not None else "note"
+
+        tags = parse_tags(metadata.get("tags", []))  # pyright: ignore
         if tags:
             metadata["tags"] = tags
-        # frontmatter
+
+        # frontmatter - use metadata with defaults applied
         entity_frontmatter = EntityFrontmatter(
-            metadata=post.metadata,
+            metadata=metadata,
         )
         entity_content = parse(post.content)
         return EntityMarkdown(

src/basic_memory/mcp/tools/__init__.py

@@ -18,7 +18,6 @@ from basic_memory.mcp.tools.canvas import canvas
 from basic_memory.mcp.tools.list_directory import list_directory
 from basic_memory.mcp.tools.edit_note import edit_note
 from basic_memory.mcp.tools.move_note import move_note
-from basic_memory.mcp.tools.sync_status import sync_status
 from basic_memory.mcp.tools.project_management import (
     list_memory_projects,
     create_memory_project,
@@ -44,7 +43,6 @@ __all__ = [
     "recent_activity",
     "search",
     "search_notes",
-    "sync_status",
     "view_note",
     "write_note",
 ]

src/basic_memory/mcp/tools/build_context.py

@@ -16,8 +16,6 @@ from basic_memory.schemas.memory import (
     memory_url_path,
 )
 
-type StringOrInt = str | int
-
 
 @mcp.tool(
     description="""Build context from a memory:// URI to continue conversations naturally.
@@ -39,7 +37,7 @@ type StringOrInt = str | int
 async def build_context(
     url: MemoryUrl,
     project: Optional[str] = None,
-    depth: Optional[StringOrInt] = 1,
+    depth: str | int | None = 1,
     timeframe: Optional[TimeFrame] = "7d",
     page: int = 1,
     page_size: int = 10,
@@ -106,28 +104,6 @@ async def build_context(
         # Get the active project using the new stateless approach
         active_project = await get_active_project(client, project, context)
 
-        # Check migration status and wait briefly if needed
-        from basic_memory.mcp.tools.utils import wait_for_migration_or_return_status
-
-        migration_status = await wait_for_migration_or_return_status(
-            timeout=5.0, project_name=active_project.name
-        )
-        if migration_status:  # pragma: no cover
-            # Return a proper GraphContext with status message
-            from basic_memory.schemas.memory import MemoryMetadata
-            from datetime import datetime
-
-            return GraphContext(
-                results=[],
-                metadata=MemoryMetadata(
-                    depth=depth or 1,
-                    timeframe=timeframe,
-                    generated_at=datetime.now().astimezone(),
-                    primary_count=0,
-                    related_count=0,
-                    uri=migration_status,  # Include status in metadata
-                ),
-            )
         project_url = active_project.project_url
 
         response = await call_get(

src/basic_memory/mcp/tools/canvas.py

@@ -110,7 +110,14 @@ async def canvas(
 
         # Write the file using the resource API
         logger.info(f"Creating canvas file: {file_path} in project {project}")
-        response = await call_put(client, f"{project_url}/resource/{file_path}", json=canvas_json)
+        # Send canvas_json as content string, not as json parameter
+        # The resource endpoint expects Body() string content, not JSON-encoded data
+        response = await call_put(
+            client,
+            f"{project_url}/resource/{file_path}",
+            content=canvas_json,
+            headers={"Content-Type": "text/plain"},
+        )
 
         # Parse response
         result = response.json()

src/basic_memory/mcp/tools/read_note.py

@@ -97,14 +97,6 @@ async def read_note(
             )
             return f"# Error\n\nIdentifier '{identifier}' is not allowed - paths must stay within project boundaries"
 
-        # Check migration status and wait briefly if needed
-        from basic_memory.mcp.tools.utils import wait_for_migration_or_return_status
-
-        migration_status = await wait_for_migration_or_return_status(
-            timeout=5.0, project_name=active_project.name
-        )
-        if migration_status:  # pragma: no cover
-            return f"# System Status\n\n{migration_status}\n\nPlease wait for migration to complete before reading notes."
         project_url = active_project.project_url
 
         # Get the file via REST API - first try direct permalink lookup

src/basic_memory/mcp/tools/search.py

@@ -205,8 +205,8 @@ async def search_notes(
     page: int = 1,
     page_size: int = 10,
     search_type: str = "text",
-    types: Optional[List[str]] = None,
-    entity_types: Optional[List[str]] = None,
+    types: List[str] = [],
+    entity_types: List[str] = [],
     after_date: Optional[str] = None,
     context: Context | None = None,
 ) -> SearchResponse | str:
@@ -345,7 +345,7 @@ async def search_notes(
     else:
         search_query.text = query  # Default to text search
 
-    # Add optional filters if provided
+    # Add optional filters if provided (empty lists are treated as no filter)
     if entity_types:
         search_query.entity_types = [SearchItemType(t) for t in entity_types]
     if types:

src/basic_memory/mcp/tools/sync_status.py

@@ -1,261 +0,0 @@
-"""Sync status tool for Basic Memory MCP server."""
-
-from typing import Optional
-
-from loguru import logger
-from fastmcp import Context
-
-from basic_memory.config import ConfigManager
-from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.server import mcp
-from basic_memory.mcp.project_context import get_active_project
-from basic_memory.services.sync_status_service import sync_status_tracker
-
-
-def _get_all_projects_status() -> list[str]:
-    """Get status lines for all configured projects."""
-    status_lines = []
-
-    try:
-        app_config = ConfigManager().config
-
-        if app_config.projects:
-            status_lines.extend(["", "---", "", "**All Projects Status:**"])
-
-            for project_name, project_path in app_config.projects.items():
-                # Check if this project has sync status
-                project_sync_status = sync_status_tracker.get_project_status(project_name)
-
-                if project_sync_status:
-                    # Project has tracked sync activity
-                    if project_sync_status.status.value == "watching":
-                        # Project is actively watching for changes (steady state)
-                        status_icon = "👁️"
-                        status_text = "Watching for changes"
-                    elif project_sync_status.status.value == "completed":
-                        # Sync completed but not yet watching - transitional state
-                        status_icon = "✅"
-                        status_text = "Sync completed"
-                    elif project_sync_status.status.value in ["scanning", "syncing"]:
-                        status_icon = "🔄"
-                        status_text = "Sync in progress"
-                        if project_sync_status.files_total > 0:
-                            progress_pct = (
-                                project_sync_status.files_processed
-                                / project_sync_status.files_total
-                            ) * 100
-                            status_text += f" ({project_sync_status.files_processed}/{project_sync_status.files_total}, {progress_pct:.0f}%)"
-                    elif project_sync_status.status.value == "failed":
-                        status_icon = "❌"
-                        status_text = f"Sync error: {project_sync_status.error or 'Unknown error'}"
-                    else:
-                        status_icon = "⏸️"
-                        status_text = project_sync_status.status.value.title()
-                else:
-                    # Project has no tracked sync activity - will be synced automatically
-                    status_icon = "⏳"
-                    status_text = "Pending sync"
-
-                status_lines.append(f"- {status_icon} **{project_name}**: {status_text}")
-
-    except Exception as e:
-        logger.debug(f"Could not get project config for comprehensive status: {e}")
-
-    return status_lines
-
-
-@mcp.tool(
-    description="""Check the status of file synchronization and background operations.
-    
-    Use this tool to:
-    - Check if file sync is in progress or completed
-    - Get detailed sync progress information  
-    - Understand if your files are fully indexed
-    - Get specific error details if sync operations failed
-    - Monitor initial project setup and legacy migration
-    
-    This covers all sync operations including:
-    - Initial project setup and file indexing
-    - Legacy project migration to unified database
-    - Ongoing file monitoring and updates
-    - Background processing of knowledge graphs
-    """,
-)
-async def sync_status(project: Optional[str] = None, context: Context | None = None) -> str:
-    """Get current sync status and system readiness information.
-
-    This tool provides detailed information about any ongoing or completed
-    sync operations, helping users understand when their files are ready.
-
-    Args:
-        project: Optional project name to get project-specific context
-
-    Returns:
-        Formatted sync status with progress, readiness, and guidance
-    """
-    logger.info("MCP tool call tool=sync_status")
-
-    async with get_client() as client:
-        status_lines = []
-
-        try:
-            from basic_memory.services.sync_status_service import sync_status_tracker
-
-            # Get overall summary
-            summary = sync_status_tracker.get_summary()
-            is_ready = sync_status_tracker.is_ready
-
-            # Header
-            status_lines.extend(
-                [
-                    "# Basic Memory Sync Status",
-                    "",
-                    f"**Current Status**: {summary}",
-                    f"**System Ready**: {'✅ Yes' if is_ready else '🔄 Processing'}",
-                    "",
-                ]
-            )
-
-            if is_ready:
-                status_lines.extend(
-                    [
-                        "✅ **All sync operations completed**",
-                        "",
-                        "- File indexing is complete",
-                        "- Knowledge graphs are up to date",
-                        "- All Basic Memory tools are fully operational",
-                        "",
-                        "Your knowledge base is ready for use!",
-                    ]
-                )
-
-                # Show all projects status even when ready
-                status_lines.extend(_get_all_projects_status())
-            else:
-                # System is still processing - show both active and all projects
-                all_sync_projects = sync_status_tracker.get_all_projects()
-
-                active_projects = [
-                    p
-                    for p in all_sync_projects.values()
-                    if p.status.value in ["scanning", "syncing"]
-                ]
-                failed_projects = [
-                    p for p in all_sync_projects.values() if p.status.value == "failed"
-                ]
-
-                if active_projects:
-                    status_lines.extend(
-                        [
-                            "🔄 **File synchronization in progress**",
-                            "",
-                            "Basic Memory is automatically processing all configured projects and building knowledge graphs.",
-                            "This typically takes 1-3 minutes depending on the amount of content.",
-                            "",
-                            "**Currently Processing:**",
-                        ]
-                    )
-
-                    for project_status in active_projects:
-                        progress = ""
-                        if project_status.files_total > 0:
-                            progress_pct = (
-                                project_status.files_processed / project_status.files_total
-                            ) * 100
-                            progress = f" ({project_status.files_processed}/{project_status.files_total}, {progress_pct:.0f}%)"
-
-                        status_lines.append(
-                            f"- **{project_status.project_name}**: {project_status.message}{progress}"
-                        )
-
-                    status_lines.extend(
-                        [
-                            "",
-                            "**What's happening:**",
-                            "- Scanning and indexing markdown files",
-                            "- Building entity and relationship graphs",
-                            "- Settings up full-text search indexes",
-                            "- Processing file changes and updates",
-                            "",
-                            "**What you can do:**",
-                            "- Wait for automatic processing to complete - no action needed",
-                            "- Use this tool again to check progress",
-                            "- Simple operations may work already",
-                            "- All projects will be available once sync finishes",
-                        ]
-                    )
-
-                # Handle failed projects (independent of active projects)
-                if failed_projects:
-                    status_lines.extend(["", "❌ **Some projects failed to sync:**", ""])
-
-                    for project_status in failed_projects:
-                        status_lines.append(
-                            f"- **{project_status.project_name}**: {project_status.error or 'Unknown error'}"
-                        )
-
-                    status_lines.extend(
-                        [
-                            "",
-                            "**Next steps:**",
-                            "1. Check the logs for detailed error information",
-                            "2. Ensure file permissions allow read/write access",
-                            "3. Try restarting the MCP server",
-                            "4. If issues persist, consider filing a support issue",
-                        ]
-                    )
-                elif not active_projects:
-                    # No active or failed projects - must be pending
-                    status_lines.extend(
-                        [
-                            "⏳ **Sync operations pending**",
-                            "",
-                            "File synchronization has been queued but hasn't started yet.",
-                            "This usually resolves automatically within a few seconds.",
-                        ]
-                    )
-
-            # Add comprehensive project status for all configured projects
-            all_projects_status = _get_all_projects_status()
-            if all_projects_status:
-                status_lines.extend(all_projects_status)
-
-                # Add explanation about automatic syncing if there are unsynced projects
-                unsynced_count = sum(1 for line in all_projects_status if "⏳" in line)
-                if unsynced_count > 0 and not is_ready:
-                    status_lines.extend(
-                        [
-                            "",
-                            "**Note**: All configured projects will be automatically synced during startup.",
-                        ]
-                    )
-
-            # Add project context if provided
-            if project:
-                try:
-                    active_project = await get_active_project(client, project, context)
-                    status_lines.extend(
-                        [
-                            "",
-                            "---",
-                            "",
-                            f"**Active Project**: {active_project.name}",
-                            f"**Project Path**: {active_project.home}",
-                        ]
-                    )
-                except Exception as e:
-                    logger.debug(f"Could not get project info: {e}")
-
-            return "\n".join(status_lines)
-
-        except Exception as e:
-            return f"""# Sync Status - Error
-
-❌ **Unable to check sync status**: {str(e)}
-
-**Troubleshooting:**
-- The system may still be starting up
-- Try waiting a few seconds and checking again
-- Check logs for detailed error information
-- Consider restarting if the issue persists
-"""

src/basic_memory/mcp/tools/utils.py

@@ -510,73 +510,3 @@ async def call_delete(
 
     except HTTPStatusError as e:
         raise ToolError(error_message) from e
-
-
-def check_migration_status() -> Optional[str]:
-    """Check if sync/migration is in progress and return status message if so.
-
-    Returns:
-        Status message if sync is in progress, None if system is ready
-    """
-    try:
-        from basic_memory.services.sync_status_service import sync_status_tracker
-
-        if not sync_status_tracker.is_ready:
-            return sync_status_tracker.get_summary()
-        return None
-    except Exception:
-        # If there's any error checking sync status, assume ready
-        return None
-
-
-async def wait_for_migration_or_return_status(
-    timeout: float = 5.0, project_name: Optional[str] = None
-) -> Optional[str]:
-    """Wait briefly for sync/migration to complete, or return status message.
-
-    Args:
-        timeout: Maximum time to wait for sync completion
-        project_name: Optional project name to check specific project status.
-                     If provided, only checks that project's readiness.
-                     If None, uses global status check (legacy behavior).
-
-    Returns:
-        Status message if sync is still in progress, None if ready
-    """
-    try:
-        from basic_memory.services.sync_status_service import sync_status_tracker
-        import asyncio
-
-        # Check if we should use project-specific or global status
-        def is_ready() -> bool:
-            if project_name:
-                return sync_status_tracker.is_project_ready(project_name)
-            return sync_status_tracker.is_ready
-
-        if is_ready():
-            return None
-
-        # Wait briefly for sync to complete
-        start_time = asyncio.get_event_loop().time()
-        while (asyncio.get_event_loop().time() - start_time) < timeout:
-            if is_ready():
-                return None
-            await asyncio.sleep(0.1)  # Check every 100ms
-
-        # Still not ready after timeout
-        if project_name:
-            # For project-specific checks, get project status details
-            project_status = sync_status_tracker.get_project_status(project_name)
-            if project_status and project_status.status.value == "failed":
-                error_msg = project_status.error or "Unknown sync error"
-                return f"❌ Sync failed for project '{project_name}': {error_msg}"
-            elif project_status:
-                return f"🔄 Project '{project_name}' is still syncing: {project_status.message}"
-            else:
-                return f"⚠️ Project '{project_name}' status unknown"
-        else:
-            # Fall back to global summary for legacy calls
-            return sync_status_tracker.get_summary()
-    except Exception:  # pragma: no cover
-        # If there's any error, assume ready
-        return None

src/basic_memory/mcp/tools/write_note.py

@@ -16,9 +16,6 @@ from basic_memory.utils import parse_tags, validate_project_path
 # Define TagType as a Union that can accept either a string or a list of strings or None
 TagType = Union[List[str], str, None]
 
-# Define TagType as a Union that can accept either a string or a list of strings or None
-TagType = Union[List[str], str, None]
-
 
 @mcp.tool(
     description="Create or update a markdown note. Returns a markdown formatted summary of the semantic content.",
@@ -28,8 +25,8 @@ async def write_note(
     content: str,
     folder: str,
     project: Optional[str] = None,
-    tags=None,
-    entity_type: str = "note",
+    tags: list[str] | str | None = None,
+    note_type: str = "note",
     context: Context | None = None,
 ) -> str:
     """Write a markdown note to the knowledge base.
@@ -70,7 +67,8 @@ async def write_note(
                 available projects.
         tags: Tags to categorize the note. Can be a list of strings, a comma-separated string, or None.
               Note: If passing from external MCP clients, use a string format (e.g. "tag1,tag2,tag3")
-        entity_type: Type of entity to create. Defaults to "note". Can be "guide", "report", "config", etc.
+        note_type: Type of note to create (stored in frontmatter). Defaults to "note".
+                   Can be "guide", "report", "config", "person", etc.
         context: Optional FastMCP context for performance caching.
 
     Returns:
@@ -96,14 +94,14 @@ async def write_note(
             content="# Weekly Standup\\n\\n- [decision] Use SQLite for storage #tech"
         )
 
-        # Create a note with tags and entity type
+        # Create a note with tags and note type
         write_note(
             project="work-project",
             title="API Design",
             folder="specs",
             content="# REST API Specification\\n\\n- implements [[Authentication]]",
             tags=["api", "design"],
-            entity_type="guide"
+            note_type="guide"
         )
 
         # Update existing note (same title/folder)
@@ -140,15 +138,6 @@ async def write_note(
             )
             return f"# Error\n\nFolder path '{folder}' is not allowed - paths must stay within project boundaries"
 
-        # Check migration status and wait briefly if needed
-        from basic_memory.mcp.tools.utils import wait_for_migration_or_return_status
-
-        migration_status = await wait_for_migration_or_return_status(
-            timeout=5.0, project_name=active_project.name
-        )
-        if migration_status:  # pragma: no cover
-            return f"# System Status\n\n{migration_status}\n\nPlease wait for migration to complete before creating notes."
-
         # Process tags using the helper function
         tag_list = parse_tags(tags)
         # Create the entity request
@@ -156,7 +145,7 @@ async def write_note(
         entity = Entity(
             title=title,
             folder=folder,
-            entity_type=entity_type,
+            entity_type=note_type,
             content_type="text/markdown",
             content=content,
             entity_metadata=metadata,

src/basic_memory/models/__init__.py

@@ -4,6 +4,7 @@ import basic_memory
 from basic_memory.models.base import Base
 from basic_memory.models.knowledge import Entity, Observation, Relation
 from basic_memory.models.project import Project
+from basic_memory.models.search import SearchIndex
 
 __all__ = [
     "Base",
@@ -11,5 +12,6 @@ __all__ = [
     "Observation",
     "Relation",
     "Project",
+    "SearchIndex",
     "basic_memory",
 ]

src/basic_memory/models/knowledge.py

@@ -13,6 +13,7 @@ from sqlalchemy import (
     DateTime,
     Index,
     JSON,
+    Float,
     text,
 )
 from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -73,6 +74,12 @@ class Entity(Base):
     # checksum of file
     checksum: Mapped[Optional[str]] = mapped_column(String, nullable=True)
 
+    # File metadata for sync
+    # mtime: file modification timestamp (Unix epoch float) for change detection
+    mtime: Mapped[Optional[float]] = mapped_column(Float, nullable=True)
+    # size: file size in bytes for quick change detection
+    size: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
+
     # Metadata and tracking
     created_at: Mapped[datetime] = mapped_column(
         DateTime(timezone=True), default=lambda: datetime.now().astimezone()

src/basic_memory/models/project.py

@@ -9,6 +9,7 @@ from sqlalchemy import (
     Text,
     Boolean,
     DateTime,
+    Float,
     Index,
     event,
 )
@@ -61,6 +62,10 @@ class Project(Base):
         onupdate=lambda: datetime.now(UTC),
     )
 
+    # Sync optimization - scan watermark tracking
+    last_scan_timestamp: Mapped[Optional[float]] = mapped_column(Float, nullable=True)
+    last_file_count: Mapped[Optional[int]] = mapped_column(Integer, nullable=True)
+
     # Define relationships to entities, observations, and relations
     # These relationships will be established once we add project_id to those models
     entities = relationship("Entity", back_populates="project", cascade="all, delete-orphan")

src/basic_memory/models/search.py

@@ -1,8 +1,56 @@
 """Search models and tables."""
 
-from sqlalchemy import DDL
+from sqlalchemy import DDL, Column, Integer, String, DateTime, Text
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.types import JSON
 
-# Define FTS5 virtual table creation
+from basic_memory.models.base import Base
+
+
+class SearchIndex(Base):
+    """Search index table for Postgres only.
+
+    For SQLite: This model is skipped; FTS5 virtual table is created via DDL instead.
+    For Postgres: This is the actual table structure with tsvector support.
+    """
+
+    __tablename__ = "search_index"
+
+    # Primary key (rowid in SQLite FTS5, explicit id in Postgres)
+    id = Column(Integer, primary_key=True, autoincrement=True)
+
+    # Core searchable fields
+    title = Column(Text, nullable=True)
+    content_stems = Column(Text, nullable=True)
+    content_snippet = Column(Text, nullable=True)
+    permalink = Column(String(255), nullable=True, index=True)
+    file_path = Column(Text, nullable=True)
+    type = Column(String(50), nullable=True)
+
+    # Project context
+    project_id = Column(Integer, nullable=True, index=True)
+
+    # Relation fields
+    from_id = Column(Integer, nullable=True)
+    to_id = Column(Integer, nullable=True)
+    relation_type = Column(String(100), nullable=True)
+
+    # Observation fields
+    entity_id = Column(Integer, nullable=True)
+    category = Column(String(100), nullable=True)
+
+    # Common fields
+    # Use JSONB for Postgres, JSON for SQLite
+    # Note: 'metadata' is a reserved name in SQLAlchemy, so we use 'metadata_' and map to 'metadata'
+    metadata_ = Column("metadata", JSON().with_variant(JSONB(), "postgresql"), nullable=True)
+    created_at = Column(DateTime(timezone=True), nullable=True)
+    updated_at = Column(DateTime(timezone=True), nullable=True)
+
+    # Note: textsearchable_index_col (tsvector) will be added by migration for Postgres only
+
+
+# Define FTS5 virtual table creation for SQLite only
+# This DDL is executed separately for SQLite databases
 CREATE_SEARCH_INDEX = DDL("""
 CREATE VIRTUAL TABLE IF NOT EXISTS search_index USING fts5(
     -- Core entity fields

src/basic_memory/repository/entity_repository.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from typing import List, Optional, Sequence, Union
 
+from loguru import logger
 from sqlalchemy import select
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
@@ -62,6 +63,55 @@ class EntityRepository(Repository[Entity]):
         )
         return await self.find_one(query)
 
+    async def get_by_file_paths_batch(
+        self, file_paths: Sequence[Union[Path, str]]
+    ) -> dict[str, Entity]:
+        """Batch fetch entities by file paths with eager-loaded relationships.
+
+        Optimized for scan operations - reduces N queries to 1 batched query.
+        Returns entities with relationships already loaded via selectinload.
+
+        Args:
+            file_paths: List of file paths to fetch entities for
+
+        Returns:
+            Dict mapping file_path (as posix string) -> Entity
+            Only includes entities that exist; missing files are not in dict
+        """
+        if not file_paths:
+            return {}
+
+        # Convert all paths to posix strings
+        posix_paths = [Path(p).as_posix() for p in file_paths]
+
+        # Batch query with eager loading
+        query = (
+            self.select().where(Entity.file_path.in_(posix_paths)).options(*self.get_load_options())
+        )
+
+        result = await self.execute_query(query)
+        entities = list(result.scalars().all())
+
+        # Return as dict for O(1) lookup
+        return {e.file_path: e for e in entities}
+
+    async def find_by_checksum(self, checksum: str) -> Sequence[Entity]:
+        """Find entities with the given checksum.
+
+        Used for move detection - finds entities that may have been moved to a new path.
+        Multiple entities may have the same checksum if files were copied.
+
+        Args:
+            checksum: File content checksum to search for
+
+        Returns:
+            Sequence of entities with matching checksum (may be empty)
+        """
+        query = self.select().where(Entity.checksum == checksum)
+        # Don't load relationships for move detection - we only need file_path and checksum
+        result = await self.execute_query(query, use_query_options=False)
+        return list(result.scalars().all())
+
     async def delete_by_file_path(self, file_path: Union[Path, str]) -> bool:
         """Delete entity with the provided file_path.
 
@@ -135,7 +185,25 @@ class EntityRepository(Repository[Entity]):
                     )
                 return found
 
-            except IntegrityError:
+            except IntegrityError as e:
+                # Check if this is a FOREIGN KEY constraint failure
+                # SQLite: "FOREIGN KEY constraint failed"
+                # Postgres: "violates foreign key constraint"
+                error_str = str(e)
+                if (
+                    "FOREIGN KEY constraint failed" in error_str
+                    or "violates foreign key constraint" in error_str
+                ):
+                    # Import locally to avoid circular dependency (repository -> services -> repository)
+                    from basic_memory.services.exceptions import SyncFatalError
+
+                    # Project doesn't exist in database - this is a fatal sync error
+                    raise SyncFatalError(
+                        f"Cannot sync file '{entity.file_path}': "
+                        f"project_id={entity.project_id} does not exist in database. "
+                        f"The project may have been deleted. This sync will be terminated."
+                    ) from e
+
                 await session.rollback()
 
                 # Re-query after rollback to get a fresh, attached entity
@@ -150,25 +218,32 @@ class EntityRepository(Repository[Entity]):
 
                 if existing_entity:
                     # File path conflict - update the existing entity
-                    for key, value in {
-                        "title": entity.title,
-                        "entity_type": entity.entity_type,
-                        "entity_metadata": entity.entity_metadata,
-                        "content_type": entity.content_type,
-                        "permalink": entity.permalink,
-                        "checksum": entity.checksum,
-                        "updated_at": entity.updated_at,
-                    }.items():
-                        setattr(existing_entity, key, value)
+                    logger.debug(
+                        f"Resolving file_path conflict for {entity.file_path}, "
+                        f"entity_id={existing_entity.id}, observations={len(entity.observations)}"
+                    )
+                    # Use merge to avoid session state conflicts
+                    # Set the ID to update existing entity
+                    entity.id = existing_entity.id
 
-                    # Clear and re-add observations
-                    existing_entity.observations.clear()
+                    # Ensure observations reference the correct entity_id
                     for obs in entity.observations:
                         obs.entity_id = existing_entity.id
-                        existing_entity.observations.append(obs)
+                        # Clear any existing ID to force INSERT as new observation
+                        obs.id = None
+
+                    # Merge the entity which will update the existing one
+                    merged_entity = await session.merge(entity)
 
                     await session.commit()
-                    return existing_entity
+
+                    # Re-query to get proper relationships loaded
+                    final_result = await session.execute(
+                        select(Entity)
+                        .where(Entity.id == merged_entity.id)
+                        .options(*self.get_load_options())
+                    )
+                    return final_result.scalar_one()
 
                 else:
                     # No file_path conflict - must be permalink conflict
@@ -176,6 +251,21 @@ class EntityRepository(Repository[Entity]):
                     entity = await self._handle_permalink_conflict(entity, session)
                     return entity
 
+    async def get_all_file_paths(self) -> List[str]:
+        """Get all file paths for this project - optimized for deletion detection.
+
+        Returns only file_path strings without loading entities or relationships.
+        Used by streaming sync to detect deleted files efficiently.
+
+        Returns:
+            List of file_path strings for all entities in the project
+        """
+        query = select(Entity.file_path)
+        query = self._add_project_filter(query)
+
+        result = await self.execute_query(query, use_query_options=False)
+        return list(result.scalars().all())
+
     async def get_distinct_directories(self) -> List[str]:
         """Extract unique directory paths from file_path column.
 
@@ -257,5 +347,103 @@ class EntityRepository(Repository[Entity]):
 
         # Insert with unique permalink
         session.add(entity)
-        await session.flush()
+        try:
+            await session.flush()
+        except IntegrityError as e:
+            # Check if this is a FOREIGN KEY constraint failure
+            # SQLite: "FOREIGN KEY constraint failed"
+            # Postgres: "violates foreign key constraint"
+            error_str = str(e)
+            if (
+                "FOREIGN KEY constraint failed" in error_str
+                or "violates foreign key constraint" in error_str
+            ):
+                # Import locally to avoid circular dependency (repository -> services -> repository)
+                from basic_memory.services.exceptions import SyncFatalError
+
+                # Project doesn't exist in database - this is a fatal sync error
+                raise SyncFatalError(
+                    f"Cannot sync file '{entity.file_path}': "
+                    f"project_id={entity.project_id} does not exist in database. "
+                    f"The project may have been deleted. This sync will be terminated."
+                ) from e
+            # Re-raise if not a foreign key error
+            raise
         return entity
+
+    async def upsert_entities(self, entities: List[Entity]) -> List[Entity]:
+        """Bulk insert or update multiple entities in a single transaction.
+
+        Optimized for batch operations with remote databases (Postgres).
+        Handles conflicts the same way as upsert_entity() but processes
+        all entities in one transaction.
+
+        Args:
+            entities: List of entities to upsert
+
+        Returns:
+            List of upserted entities with relationships loaded
+
+        Raises:
+            SyncFatalError: If any entity references a non-existent project_id
+        """
+        if not entities:
+            return []
+
+        async with db.scoped_session(self.session_maker) as session:
+            # Set project_id on all entities if needed
+            for entity in entities:
+                self._set_project_id_if_needed(entity)
+
+            # Try to add all entities
+            for entity in entities:
+                session.add(entity)
+
+            try:
+                await session.flush()
+
+                # Fetch all entities with relationships loaded
+                file_paths = [e.file_path for e in entities]
+                query = (
+                    self.select()
+                    .where(Entity.file_path.in_(file_paths))
+                    .options(*self.get_load_options())
+                )
+                result = await session.execute(query)
+                return list(result.scalars().all())
+
+            except IntegrityError as e:
+                # Check for foreign key constraint failures
+                error_str = str(e)
+                if (
+                    "FOREIGN KEY constraint failed" in error_str
+                    or "violates foreign key constraint" in error_str
+                ):
+                    from basic_memory.services.exceptions import SyncFatalError
+
+                    raise SyncFatalError(
+                        "Cannot sync entities: project_id does not exist in database. "
+                        "The project may have been deleted. This sync will be terminated."
+                    ) from e
+
+                # For other integrity errors (file_path or permalink conflicts),
+                # rollback and fall back to individual processing
+                await session.rollback()
+
+                # Process each entity individually to handle conflicts properly
+                logger.debug(
+                    f"Batch upsert failed with IntegrityError, falling back to individual upserts for {len(entities)} entities"
+                )
+
+                result_entities = []
+                for entity in entities:
+                    try:
+                        upserted = await self.upsert_entity(entity)
+                        result_entities.append(upserted)
+                    except Exception as individual_error:
+                        logger.error(
+                            f"Failed to upsert entity {entity.file_path}: {individual_error}"
+                        )
+                        # Continue with other entities
+
+                return result_entities

src/basic_memory/repository/observation_repository.py

@@ -70,3 +70,33 @@ class ObservationRepository(Repository[Observation]):
             observations_by_entity[obs.entity_id].append(obs)
 
         return observations_by_entity
+
+    async def delete_by_entity_ids(self, entity_ids: List[int]) -> int:
+        """Delete all observations for multiple entities in a single query.
+
+        Optimized for batch operations - deletes observations for many entities
+        in one database transaction.
+
+        Args:
+            entity_ids: List of entity IDs whose observations should be deleted
+
+        Returns:
+            Number of observations deleted
+        """
+        if not entity_ids:
+            return 0
+
+        from basic_memory import db
+
+        async with db.scoped_session(self.session_maker) as session:
+            # Use bulk delete with IN clause
+            query = select(Observation).where(Observation.entity_id.in_(entity_ids))
+            result = await session.execute(query)
+            observations_to_delete = result.scalars().all()
+
+            # Delete all observations
+            for obs in observations_to_delete:
+                await session.delete(obs)
+
+            await session.flush()
+            return len(observations_to_delete)

src/basic_memory/repository/postgres_search_repository.py

@@ -0,0 +1,313 @@
+"""PostgreSQL tsvector-based search repository implementation."""
+
+import json
+import re
+from datetime import datetime
+from typing import List, Optional
+
+from loguru import logger
+from sqlalchemy import text
+
+from basic_memory import db
+from basic_memory.repository.search_index_row import SearchIndexRow
+from basic_memory.repository.search_repository_base import SearchRepositoryBase
+from basic_memory.schemas.search import SearchItemType
+
+
+class PostgresSearchRepository(SearchRepositoryBase):
+    """PostgreSQL tsvector implementation of search repository.
+
+    Uses PostgreSQL's full-text search capabilities with:
+    - tsvector for document representation
+    - tsquery for query representation
+    - GIN indexes for performance
+    - ts_rank() function for relevance scoring
+    - JSONB containment operators for metadata search
+    """
+
+    async def init_search_index(self):
+        """Create Postgres table with tsvector column and GIN indexes.
+
+        Note: This is handled by Alembic migrations. This method is a no-op
+        for Postgres as the schema is created via migrations.
+        """
+        logger.info("PostgreSQL search index initialization handled by migrations")
+        # Table creation is done via Alembic migrations
+        # This includes:
+        # - CREATE TABLE search_index (...)
+        # - ADD COLUMN textsearchable_index_col tsvector GENERATED ALWAYS AS (...)
+        # - CREATE INDEX USING GIN on textsearchable_index_col
+        # - CREATE INDEX USING GIN on metadata jsonb_path_ops
+        pass
+
+    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a search term for tsquery format.
+
+        Args:
+            term: The search term to prepare
+            is_prefix: Whether to add prefix search capability (:* operator)
+
+        Returns:
+            Formatted search term for tsquery
+
+        For Postgres:
+        - Boolean operators are converted to tsquery format (&, |, !)
+        - Prefix matching uses the :* operator
+        - Terms are sanitized to prevent tsquery syntax errors
+        """
+        # Check for explicit boolean operators
+        boolean_operators = [" AND ", " OR ", " NOT "]
+        if any(op in f" {term} " for op in boolean_operators):
+            return self._prepare_boolean_query(term)
+
+        # For non-Boolean queries, prepare single term
+        return self._prepare_single_term(term, is_prefix)
+
+    def _prepare_boolean_query(self, query: str) -> str:
+        """Convert Boolean query to tsquery format.
+
+        Args:
+            query: A Boolean query like "coffee AND brewing" or "(pour OR french) AND press"
+
+        Returns:
+            tsquery-formatted string with & (AND), | (OR), ! (NOT) operators
+
+        Examples:
+            "coffee AND brewing" -> "coffee & brewing"
+            "(pour OR french) AND press" -> "(pour | french) & press"
+            "coffee NOT decaf" -> "coffee & !decaf"
+        """
+        # Replace Boolean operators with tsquery operators
+        # Keep parentheses for grouping
+        result = query
+        result = re.sub(r"\bAND\b", "&", result)
+        result = re.sub(r"\bOR\b", "|", result)
+        # NOT must be converted to "& !" and the ! must be attached to the following term
+        # "Python NOT Django" -> "Python & !Django"
+        result = re.sub(r"\bNOT\s+", "& !", result)
+
+        return result
+
+    def _prepare_single_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a single search term for tsquery.
+
+        Args:
+            term: A single search term
+            is_prefix: Whether to add prefix search capability (:* suffix)
+
+        Returns:
+            A properly formatted single term for tsquery
+
+        For Postgres tsquery:
+        - Multi-word queries become "word1 & word2"
+        - Prefix matching uses ":*" suffix (e.g., "coff:*")
+        - Special characters that need escaping: & | ! ( ) :
+        """
+        if not term or not term.strip():
+            return term
+
+        term = term.strip()
+
+        # Check if term is already a wildcard pattern
+        if "*" in term:
+            # Replace * with :* for Postgres prefix matching
+            return term.replace("*", ":*")
+
+        # Remove tsquery special characters from the search term
+        # These characters have special meaning in tsquery and cause syntax errors
+        # if not used as operators
+        special_chars = ["&", "|", "!", "(", ")", ":"]
+        cleaned_term = term
+        for char in special_chars:
+            cleaned_term = cleaned_term.replace(char, " ")
+
+        # Handle multi-word queries
+        if " " in cleaned_term:
+            words = [w for w in cleaned_term.split() if w.strip()]
+            if not words:
+                # All characters were special chars, search won't match anything
+                # Return a safe search term that won't cause syntax errors
+                return "NOSPECIALCHARS:*"
+            if is_prefix:
+                # Add prefix matching to each word
+                prepared_words = [f"{word}:*" for word in words]
+            else:
+                prepared_words = words
+            # Join with AND operator
+            return " & ".join(prepared_words)
+
+        # Single word
+        cleaned_term = cleaned_term.strip()
+        if not cleaned_term:
+            return "NOSPECIALCHARS:*"
+        if is_prefix:
+            return f"{cleaned_term}:*"
+        else:
+            return cleaned_term
+
+    async def search(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        limit: int = 10,
+        offset: int = 0,
+    ) -> List[SearchIndexRow]:
+        """Search across all indexed content using PostgreSQL tsvector."""
+        conditions = []
+        params = {}
+        order_by_clause = ""
+
+        # Handle text search for title and content using tsvector
+        if search_text:
+            if search_text.strip() == "*" or search_text.strip() == "":
+                # For wildcard searches, don't add any text conditions
+                pass
+            else:
+                # Prepare search term for tsquery
+                processed_text = self._prepare_search_term(search_text.strip())
+                params["text"] = processed_text
+                # Use @@ operator for tsvector matching
+                conditions.append("textsearchable_index_col @@ to_tsquery('english', :text)")
+
+        # Handle title search
+        if title:
+            title_text = self._prepare_search_term(title.strip(), is_prefix=False)
+            params["title_text"] = title_text
+            conditions.append("to_tsvector('english', title) @@ to_tsquery('english', :title_text)")
+
+        # Handle permalink exact search
+        if permalink:
+            params["permalink"] = permalink
+            conditions.append("permalink = :permalink")
+
+        # Handle permalink pattern match
+        if permalink_match:
+            permalink_text = permalink_match.lower().strip()
+            params["permalink"] = permalink_text
+            if "*" in permalink_match:
+                # Use LIKE for pattern matching in Postgres
+                # Convert * to % for SQL LIKE
+                permalink_pattern = permalink_text.replace("*", "%")
+                params["permalink"] = permalink_pattern
+                conditions.append("permalink LIKE :permalink")
+            else:
+                conditions.append("permalink = :permalink")
+
+        # Handle search item type filter
+        if search_item_types:
+            type_list = ", ".join(f"'{t.value}'" for t in search_item_types)
+            conditions.append(f"type IN ({type_list})")
+
+        # Handle entity type filter using JSONB containment
+        if types:
+            # Use JSONB @> operator for efficient containment queries
+            type_conditions = []
+            for entity_type in types:
+                # Create JSONB containment condition for each type
+                type_conditions.append(f'metadata @> \'{{"entity_type": "{entity_type}"}}\'')
+            conditions.append(f"({' OR '.join(type_conditions)})")
+
+        # Handle date filter
+        if after_date:
+            params["after_date"] = after_date
+            conditions.append("created_at > :after_date")
+            # order by most recent first
+            order_by_clause = ", updated_at DESC"
+
+        # Always filter by project_id
+        params["project_id"] = self.project_id
+        conditions.append("project_id = :project_id")
+
+        # set limit and offset
+        params["limit"] = limit
+        params["offset"] = offset
+
+        # Build WHERE clause
+        where_clause = " AND ".join(conditions) if conditions else "1=1"
+
+        # Build SQL with ts_rank() for scoring
+        # Note: If no text search, score will be NULL, so we use COALESCE to default to 0
+        if search_text and search_text.strip() and search_text.strip() != "*":
+            score_expr = "ts_rank(textsearchable_index_col, to_tsquery('english', :text))"
+        else:
+            score_expr = "0"
+
+        sql = f"""
+            SELECT
+                project_id,
+                id,
+                title,
+                permalink,
+                file_path,
+                type,
+                metadata,
+                from_id,
+                to_id,
+                relation_type,
+                entity_id,
+                content_snippet,
+                category,
+                created_at,
+                updated_at,
+                {score_expr} as score
+            FROM search_index
+            WHERE {where_clause}
+            ORDER BY score DESC {order_by_clause}
+            LIMIT :limit
+            OFFSET :offset
+        """
+
+        logger.trace(f"Search {sql} params: {params}")
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                result = await session.execute(text(sql), params)
+                rows = result.fetchall()
+        except Exception as e:
+            # Handle tsquery syntax errors
+            if "tsquery" in str(e).lower() or "syntax error" in str(e).lower():  # pragma: no cover
+                logger.warning(f"tsquery syntax error for search term: {search_text}, error: {e}")
+                # Return empty results rather than crashing
+                return []
+            else:
+                # Re-raise other database errors
+                logger.error(f"Database error during search: {e}")
+                raise
+
+        results = [
+            SearchIndexRow(
+                project_id=self.project_id,
+                id=row.id,
+                title=row.title,
+                permalink=row.permalink,
+                file_path=row.file_path,
+                type=row.type,
+                score=float(row.score) if row.score else 0.0,
+                metadata=(
+                    row.metadata
+                    if isinstance(row.metadata, dict)
+                    else (json.loads(row.metadata) if row.metadata else {})
+                ),
+                from_id=row.from_id,
+                to_id=row.to_id,
+                relation_type=row.relation_type,
+                entity_id=row.entity_id,
+                content_snippet=row.content_snippet,
+                category=row.category,
+                created_at=row.created_at,
+                updated_at=row.updated_at,
+            )
+            for row in rows
+        ]
+
+        logger.trace(f"Found {len(results)} search results")
+        for r in results:
+            logger.trace(
+                f"Search result: project_id: {r.project_id} type:{r.type} title: {r.title} permalink: {r.permalink} score: {r.score}"
+            )
+
+        return results

src/basic_memory/repository/relation_repository.py

@@ -67,6 +67,27 @@ class RelationRepository(Repository[Relation]):
         async with db.scoped_session(self.session_maker) as session:
             await session.execute(delete(Relation).where(Relation.from_id == entity_id))
 
+    async def delete_outgoing_relations_from_entities(self, entity_ids: List[int]) -> int:
+        """Delete outgoing relations for multiple entities in a single query.
+
+        Optimized for batch operations - deletes relations for many entities
+        in one database transaction. Only deletes relations where these entities
+        are the source (from_id).
+
+        Args:
+            entity_ids: List of entity IDs whose outgoing relations should be deleted
+
+        Returns:
+            Number of relations deleted
+        """
+        if not entity_ids:
+            return 0
+
+        async with db.scoped_session(self.session_maker) as session:
+            # Use bulk delete with IN clause
+            result = await session.execute(delete(Relation).where(Relation.from_id.in_(entity_ids)))
+            return result.rowcount or 0
+
     async def find_unresolved_relations(self) -> Sequence[Relation]:
         """Find all unresolved relations, where to_id is null."""
         query = select(Relation).filter(Relation.to_id.is_(None))

src/basic_memory/repository/search_index_row.py

@@ -0,0 +1,95 @@
+"""Search index data structures."""
+
+import json
+from dataclasses import dataclass
+from datetime import datetime
+from typing import Optional
+from pathlib import Path
+
+from basic_memory.schemas.search import SearchItemType
+
+
+@dataclass
+class SearchIndexRow:
+    """Search result with score and metadata."""
+
+    project_id: int
+    id: int
+    type: str
+    file_path: str
+
+    # date values
+    created_at: datetime
+    updated_at: datetime
+
+    permalink: Optional[str] = None
+    metadata: Optional[dict] = None
+
+    # assigned in result
+    score: Optional[float] = None
+
+    # Type-specific fields
+    title: Optional[str] = None  # entity
+    content_stems: Optional[str] = None  # entity, observation
+    content_snippet: Optional[str] = None  # entity, observation
+    entity_id: Optional[int] = None  # observations
+    category: Optional[str] = None  # observations
+    from_id: Optional[int] = None  # relations
+    to_id: Optional[int] = None  # relations
+    relation_type: Optional[str] = None  # relations
+
+    @property
+    def content(self):
+        return self.content_snippet
+
+    @property
+    def directory(self) -> str:
+        """Extract directory part from file_path.
+
+        For a file at "projects/notes/ideas.md", returns "/projects/notes"
+        For a file at root level "README.md", returns "/"
+        """
+        if not self.type == SearchItemType.ENTITY.value and not self.file_path:
+            return ""
+
+        # Normalize path separators to handle both Windows (\) and Unix (/) paths
+        normalized_path = Path(self.file_path).as_posix()
+
+        # Split the path by slashes
+        parts = normalized_path.split("/")
+
+        # If there's only one part (e.g., "README.md"), it's at the root
+        if len(parts) <= 1:
+            return "/"
+
+        # Join all parts except the last one (filename)
+        directory_path = "/".join(parts[:-1])
+        return f"/{directory_path}"
+
+    def to_insert(self, serialize_json: bool = True):
+        """Convert to dict for database insertion.
+
+        Args:
+            serialize_json: If True, converts metadata dict to JSON string (for SQLite).
+                           If False, keeps metadata as dict (for Postgres JSONB).
+        """
+        return {
+            "id": self.id,
+            "title": self.title,
+            "content_stems": self.content_stems,
+            "content_snippet": self.content_snippet,
+            "permalink": self.permalink,
+            "file_path": self.file_path,
+            "type": self.type,
+            "metadata": json.dumps(self.metadata)
+            if serialize_json and self.metadata
+            else self.metadata,
+            "from_id": self.from_id,
+            "to_id": self.to_id,
+            "relation_type": self.relation_type,
+            "entity_id": self.entity_id,
+            "category": self.category,
+            "created_at": self.created_at if self.created_at else None,
+            "updated_at": self.updated_at if self.updated_at else None,
+            "project_id": self.project_id,
+        }

src/basic_memory/repository/search_repository.py

@@ -1,365 +1,35 @@
-"""Repository for search operations."""
+"""Repository for search operations.
+
+This module provides the search repository interface.
+The actual repository implementations are backend-specific:
+- SQLiteSearchRepository: Uses FTS5 virtual tables
+- PostgresSearchRepository: Uses tsvector/tsquery with GIN indexes
+"""
 
-import json
-import re
-import time
-from dataclasses import dataclass
 from datetime import datetime
-from typing import Any, Dict, List, Optional
-from pathlib import Path
+from typing import List, Optional, Protocol
 
-from loguru import logger
-from sqlalchemy import Executable, Result, text
+from sqlalchemy import Result
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
-from basic_memory import db
-from basic_memory.models.search import CREATE_SEARCH_INDEX
+from basic_memory.config import ConfigManager, DatabaseBackend
+from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
+from basic_memory.repository.search_index_row import SearchIndexRow
+from basic_memory.repository.sqlite_search_repository import SQLiteSearchRepository
 from basic_memory.schemas.search import SearchItemType
 
 
-@dataclass
-class SearchIndexRow:
-    """Search result with score and metadata."""
+class SearchRepository(Protocol):
+    """Protocol defining the search repository interface.
+
+    Both SQLite and Postgres implementations must satisfy this protocol.
+    """
 
     project_id: int
-    id: int
-    type: str
-    file_path: str
 
-    # date values
-    created_at: datetime
-    updated_at: datetime
-
-    permalink: Optional[str] = None
-    metadata: Optional[dict] = None
-
-    # assigned in result
-    score: Optional[float] = None
-
-    # Type-specific fields
-    title: Optional[str] = None  # entity
-    content_stems: Optional[str] = None  # entity, observation
-    content_snippet: Optional[str] = None  # entity, observation
-    entity_id: Optional[int] = None  # observations
-    category: Optional[str] = None  # observations
-    from_id: Optional[int] = None  # relations
-    to_id: Optional[int] = None  # relations
-    relation_type: Optional[str] = None  # relations
-
-    @property
-    def content(self):
-        return self.content_snippet
-
-    @property
-    def directory(self) -> str:
-        """Extract directory part from file_path.
-
-        For a file at "projects/notes/ideas.md", returns "/projects/notes"
-        For a file at root level "README.md", returns "/"
-        """
-        if not self.type == SearchItemType.ENTITY.value and not self.file_path:
-            return ""
-
-        # Normalize path separators to handle both Windows (\) and Unix (/) paths
-        normalized_path = Path(self.file_path).as_posix()
-
-        # Split the path by slashes
-        parts = normalized_path.split("/")
-
-        # If there's only one part (e.g., "README.md"), it's at the root
-        if len(parts) <= 1:
-            return "/"
-
-        # Join all parts except the last one (filename)
-        directory_path = "/".join(parts[:-1])
-        return f"/{directory_path}"
-
-    def to_insert(self):
-        return {
-            "id": self.id,
-            "title": self.title,
-            "content_stems": self.content_stems,
-            "content_snippet": self.content_snippet,
-            "permalink": self.permalink,
-            "file_path": self.file_path,
-            "type": self.type,
-            "metadata": json.dumps(self.metadata),
-            "from_id": self.from_id,
-            "to_id": self.to_id,
-            "relation_type": self.relation_type,
-            "entity_id": self.entity_id,
-            "category": self.category,
-            "created_at": self.created_at if self.created_at else None,
-            "updated_at": self.updated_at if self.updated_at else None,
-            "project_id": self.project_id,
-        }
-
-
-class SearchRepository:
-    """Repository for search index operations."""
-
-    def __init__(self, session_maker: async_sessionmaker[AsyncSession], project_id: int):
-        """Initialize with session maker and project_id filter.
-
-        Args:
-            session_maker: SQLAlchemy session maker
-            project_id: Project ID to filter all operations by
-
-        Raises:
-            ValueError: If project_id is None or invalid
-        """
-        if project_id is None or project_id <= 0:  # pragma: no cover
-            raise ValueError("A valid project_id is required for SearchRepository")
-
-        self.session_maker = session_maker
-        self.project_id = project_id
-
-    async def init_search_index(self):
-        """Create or recreate the search index."""
-        logger.info("Initializing search index")
-        try:
-            async with db.scoped_session(self.session_maker) as session:
-                await session.execute(CREATE_SEARCH_INDEX)
-                await session.commit()
-        except Exception as e:  # pragma: no cover
-            logger.error(f"Error initializing search index: {e}")
-            raise e
-
-    def _prepare_boolean_query(self, query: str) -> str:
-        """Prepare a Boolean query by quoting individual terms while preserving operators.
-
-        Args:
-            query: A Boolean query like "tier1-test AND unicode" or "(hello OR world) NOT test"
-
-        Returns:
-            A properly formatted Boolean query with quoted terms that need quoting
-        """
-        # Define Boolean operators and their boundaries
-        boolean_pattern = r"(\bAND\b|\bOR\b|\bNOT\b)"
-
-        # Split the query by Boolean operators, keeping the operators
-        parts = re.split(boolean_pattern, query)
-
-        processed_parts = []
-        for part in parts:
-            part = part.strip()
-            if not part:
-                continue
-
-            # If it's a Boolean operator, keep it as is
-            if part in ["AND", "OR", "NOT"]:
-                processed_parts.append(part)
-            else:
-                # Handle parentheses specially - they should be preserved for grouping
-                if "(" in part or ")" in part:
-                    # Parse parenthetical expressions carefully
-                    processed_part = self._prepare_parenthetical_term(part)
-                    processed_parts.append(processed_part)
-                else:
-                    # This is a search term - for Boolean queries, don't add prefix wildcards
-                    prepared_term = self._prepare_single_term(part, is_prefix=False)
-                    processed_parts.append(prepared_term)
-
-        return " ".join(processed_parts)
-
-    def _prepare_parenthetical_term(self, term: str) -> str:
-        """Prepare a term that contains parentheses, preserving the parentheses for grouping.
-
-        Args:
-            term: A term that may contain parentheses like "(hello" or "world)" or "(hello OR world)"
-
-        Returns:
-            A properly formatted term with parentheses preserved
-        """
-        # Handle terms that start/end with parentheses but may contain quotable content
-        result = ""
-        i = 0
-        while i < len(term):
-            if term[i] in "()":
-                # Preserve parentheses as-is
-                result += term[i]
-                i += 1
-            else:
-                # Find the next parenthesis or end of string
-                start = i
-                while i < len(term) and term[i] not in "()":
-                    i += 1
-
-                # Extract the content between parentheses
-                content = term[start:i].strip()
-                if content:
-                    # Only quote if it actually needs quoting (has hyphens, special chars, etc)
-                    # but don't quote if it's just simple words
-                    if self._needs_quoting(content):
-                        escaped_content = content.replace('"', '""')
-                        result += f'"{escaped_content}"'
-                    else:
-                        result += content
-
-        return result
-
-    def _needs_quoting(self, term: str) -> bool:
-        """Check if a term needs to be quoted for FTS5 safety.
-
-        Args:
-            term: The term to check
-
-        Returns:
-            True if the term should be quoted
-        """
-        if not term or not term.strip():
-            return False
-
-        # Characters that indicate we should quote (excluding parentheses which are valid syntax)
-        needs_quoting_chars = [
-            " ",
-            ".",
-            ":",
-            ";",
-            ",",
-            "<",
-            ">",
-            "?",
-            "/",
-            "-",
-            "'",
-            '"',
-            "[",
-            "]",
-            "{",
-            "}",
-            "+",
-            "!",
-            "@",
-            "#",
-            "$",
-            "%",
-            "^",
-            "&",
-            "=",
-            "|",
-            "\\",
-            "~",
-            "`",
-        ]
-
-        return any(c in term for c in needs_quoting_chars)
-
-    def _prepare_single_term(self, term: str, is_prefix: bool = True) -> str:
-        """Prepare a single search term (no Boolean operators).
-
-        Args:
-            term: A single search term
-            is_prefix: Whether to add prefix search capability (* suffix)
-
-        Returns:
-            A properly formatted single term
-        """
-        if not term or not term.strip():
-            return term
-
-        term = term.strip()
-
-        # Check if term is already a proper wildcard pattern (alphanumeric + *)
-        # e.g., "hello*", "test*world" - these should be left alone
-        if "*" in term and all(c.isalnum() or c in "*_-" for c in term):
-            return term
-
-        # Characters that can cause FTS5 syntax errors when used as operators
-        # We're more conservative here - only quote when we detect problematic patterns
-        problematic_chars = [
-            '"',
-            "'",
-            "(",
-            ")",
-            "[",
-            "]",
-            "{",
-            "}",
-            "+",
-            "!",
-            "@",
-            "#",
-            "$",
-            "%",
-            "^",
-            "&",
-            "=",
-            "|",
-            "\\",
-            "~",
-            "`",
-        ]
-
-        # Characters that indicate we should quote (spaces, dots, colons, etc.)
-        # Adding hyphens here because FTS5 can have issues with hyphens followed by wildcards
-        needs_quoting_chars = [" ", ".", ":", ";", ",", "<", ">", "?", "/", "-"]
-
-        # Check if term needs quoting
-        has_problematic = any(c in term for c in problematic_chars)
-        has_spaces_or_special = any(c in term for c in needs_quoting_chars)
-
-        if has_problematic or has_spaces_or_special:
-            # Handle multi-word queries differently from special character queries
-            if " " in term and not any(c in term for c in problematic_chars):
-                # Check if any individual word contains special characters that need quoting
-                words = term.strip().split()
-                has_special_in_words = any(
-                    any(c in word for c in needs_quoting_chars if c != " ") for word in words
-                )
-
-                if not has_special_in_words:
-                    # For multi-word queries with simple words (like "emoji unicode"),
-                    # use boolean AND to handle word order variations
-                    if is_prefix:
-                        # Add prefix wildcard to each word for better matching
-                        prepared_words = [f"{word}*" for word in words if word]
-                    else:
-                        prepared_words = words
-                    term = " AND ".join(prepared_words)
-                else:
-                    # If any word has special characters, quote the entire phrase
-                    escaped_term = term.replace('"', '""')
-                    if is_prefix and not ("/" in term and term.endswith(".md")):
-                        term = f'"{escaped_term}"*'
-                    else:
-                        term = f'"{escaped_term}"'
-            else:
-                # For terms with problematic characters or file paths, use exact phrase matching
-                # Escape any existing quotes by doubling them
-                escaped_term = term.replace('"', '""')
-                # Quote the entire term to handle special characters safely
-                if is_prefix and not ("/" in term and term.endswith(".md")):
-                    # For search terms (not file paths), add prefix matching
-                    term = f'"{escaped_term}"*'
-                else:
-                    # For file paths, use exact matching
-                    term = f'"{escaped_term}"'
-        elif is_prefix:
-            # Only add wildcard for simple terms without special characters
-            term = f"{term}*"
-
-        return term
-
-    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
-        """Prepare a search term for FTS5 query.
-
-        Args:
-            term: The search term to prepare
-            is_prefix: Whether to add prefix search capability (* suffix)
-
-        For FTS5:
-        - Boolean operators (AND, OR, NOT) are preserved for complex queries
-        - Terms with FTS5 special characters are quoted to prevent syntax errors
-        - Simple terms get prefix wildcards for better matching
-        """
-        # Check for explicit boolean operators - if present, process as Boolean query
-        boolean_operators = [" AND ", " OR ", " NOT "]
-        if any(op in f" {term} " for op in boolean_operators):
-            return self._prepare_boolean_query(term)
-
-        # For non-Boolean queries, use the single term preparation logic
-        return self._prepare_single_term(term, is_prefix)
+    async def init_search_index(self) -> None:
+        """Initialize the search index schema."""
+        ...
 
     async def search(
         self,
@@ -373,267 +43,52 @@ class SearchRepository:
         limit: int = 10,
         offset: int = 0,
     ) -> List[SearchIndexRow]:
-        """Search across all indexed content with fuzzy matching."""
-        conditions = []
-        params = {}
-        order_by_clause = ""
+        """Search across indexed content."""
+        ...
 
-        # Handle text search for title and content
-        if search_text:
-            # Skip FTS for wildcard-only queries that would cause "unknown special query" errors
-            if search_text.strip() == "*" or search_text.strip() == "":
-                # For wildcard searches, don't add any text conditions - return all results
-                pass
-            else:
-                # Use _prepare_search_term to handle both Boolean and non-Boolean queries
-                processed_text = self._prepare_search_term(search_text.strip())
-                params["text"] = processed_text
-                conditions.append("(title MATCH :text OR content_stems MATCH :text)")
+    async def index_item(self, search_index_row: SearchIndexRow) -> None:
+        """Index a single item."""
+        ...
 
-        # Handle title match search
-        if title:
-            title_text = self._prepare_search_term(title.strip(), is_prefix=False)
-            params["title_text"] = title_text
-            conditions.append("title MATCH :title_text")
+    async def bulk_index_items(self, search_index_rows: List[SearchIndexRow]) -> None:
+        """Index multiple items in a batch."""
+        ...
 
-        # Handle permalink exact search
-        if permalink:
-            params["permalink"] = permalink
-            conditions.append("permalink = :permalink")
+    async def delete_by_permalink(self, permalink: str) -> None:
+        """Delete item by permalink."""
+        ...
 
-        # Handle permalink match search, supports *
-        if permalink_match:
-            # For GLOB patterns, don't use _prepare_search_term as it will quote slashes
-            # GLOB patterns need to preserve their syntax
-            permalink_text = permalink_match.lower().strip()
-            params["permalink"] = permalink_text
-            if "*" in permalink_match:
-                conditions.append("permalink GLOB :permalink")
-            else:
-                # For exact matches without *, we can use FTS5 MATCH
-                # but only prepare the term if it doesn't look like a path
-                if "/" in permalink_text:
-                    conditions.append("permalink = :permalink")
-                else:
-                    permalink_text = self._prepare_search_term(permalink_text, is_prefix=False)
-                    params["permalink"] = permalink_text
-                    conditions.append("permalink MATCH :permalink")
+    async def delete_by_entity_id(self, entity_id: int) -> None:
+        """Delete items by entity ID."""
+        ...
 
-        # Handle entity type filter
-        if search_item_types:
-            type_list = ", ".join(f"'{t.value}'" for t in search_item_types)
-            conditions.append(f"type IN ({type_list})")
+    async def execute_query(self, query, params: dict) -> Result:
+        """Execute a raw SQL query."""
+        ...
 
-        # Handle type filter
-        if types:
-            type_list = ", ".join(f"'{t}'" for t in types)
-            conditions.append(f"json_extract(metadata, '$.entity_type') IN ({type_list})")
 
-        # Handle date filter using datetime() for proper comparison
-        if after_date:
-            params["after_date"] = after_date
-            conditions.append("datetime(created_at) > datetime(:after_date)")
+def create_search_repository(
+    session_maker: async_sessionmaker[AsyncSession], project_id: int
+) -> SearchRepository:
+    """Factory function to create the appropriate search repository based on database backend.
 
-            # order by most recent first
-            order_by_clause = ", updated_at DESC"
+    Args:
+        session_maker: SQLAlchemy async session maker
+        project_id: Project ID for the repository
 
-        # Always filter by project_id
-        params["project_id"] = self.project_id
-        conditions.append("project_id = :project_id")
+    Returns:
+        SearchRepository: Backend-appropriate search repository instance
+    """
+    config = ConfigManager().config
 
-        # set limit on search query
-        params["limit"] = limit
-        params["offset"] = offset
+    if config.database_backend == DatabaseBackend.POSTGRES:
+        return PostgresSearchRepository(session_maker, project_id=project_id)
+    else:
+        return SQLiteSearchRepository(session_maker, project_id=project_id)
 
-        # Build WHERE clause
-        where_clause = " AND ".join(conditions) if conditions else "1=1"
 
-        sql = f"""
-            SELECT 
-                project_id,
-                id, 
-                title, 
-                permalink,
-                file_path,
-                type,
-                metadata,
-                from_id,
-                to_id,
-                relation_type,
-                entity_id,
-                content_snippet,
-                category,
-                created_at,
-                updated_at,
-                bm25(search_index) as score
-            FROM search_index 
-            WHERE {where_clause}
-            ORDER BY score ASC {order_by_clause}
-            LIMIT :limit
-            OFFSET :offset
-        """
-
-        logger.trace(f"Search {sql} params: {params}")
-        try:
-            async with db.scoped_session(self.session_maker) as session:
-                result = await session.execute(text(sql), params)
-                rows = result.fetchall()
-        except Exception as e:
-            # Handle FTS5 syntax errors and provide user-friendly feedback
-            if "fts5: syntax error" in str(e).lower():  # pragma: no cover
-                logger.warning(f"FTS5 syntax error for search term: {search_text}, error: {e}")
-                # Return empty results rather than crashing
-                return []
-            else:
-                # Re-raise other database errors
-                logger.error(f"Database error during search: {e}")
-                raise
-
-        results = [
-            SearchIndexRow(
-                project_id=self.project_id,
-                id=row.id,
-                title=row.title,
-                permalink=row.permalink,
-                file_path=row.file_path,
-                type=row.type,
-                score=row.score,
-                metadata=json.loads(row.metadata),
-                from_id=row.from_id,
-                to_id=row.to_id,
-                relation_type=row.relation_type,
-                entity_id=row.entity_id,
-                content_snippet=row.content_snippet,
-                category=row.category,
-                created_at=row.created_at,
-                updated_at=row.updated_at,
-            )
-            for row in rows
-        ]
-
-        logger.trace(f"Found {len(results)} search results")
-        for r in results:
-            logger.trace(
-                f"Search result: project_id: {r.project_id} type:{r.type} title: {r.title} permalink: {r.permalink} score: {r.score}"
-            )
-
-        return results
-
-    async def index_item(
-        self,
-        search_index_row: SearchIndexRow,
-    ):
-        """Index or update a single item."""
-        async with db.scoped_session(self.session_maker) as session:
-            # Delete existing record if any
-            await session.execute(
-                text(
-                    "DELETE FROM search_index WHERE permalink = :permalink AND project_id = :project_id"
-                ),
-                {"permalink": search_index_row.permalink, "project_id": self.project_id},
-            )
-
-            # Prepare data for insert with project_id
-            insert_data = search_index_row.to_insert()
-            insert_data["project_id"] = self.project_id
-
-            # Insert new record
-            await session.execute(
-                text("""
-                    INSERT INTO search_index (
-                        id, title, content_stems, content_snippet, permalink, file_path, type, metadata,
-                        from_id, to_id, relation_type,
-                        entity_id, category,
-                        created_at, updated_at,
-                        project_id
-                    ) VALUES (
-                        :id, :title, :content_stems, :content_snippet, :permalink, :file_path, :type, :metadata,
-                        :from_id, :to_id, :relation_type,
-                        :entity_id, :category,
-                        :created_at, :updated_at,
-                        :project_id
-                    )
-                """),
-                insert_data,
-            )
-            logger.debug(f"indexed row {search_index_row}")
-            await session.commit()
-
-    async def bulk_index_items(self, search_index_rows: List[SearchIndexRow]):
-        """Index multiple items in a single batch operation.
-
-        Note: This method assumes that any existing records for the entity_id
-        have already been deleted (typically via delete_by_entity_id).
-
-        Args:
-            search_index_rows: List of SearchIndexRow objects to index
-        """
-        if not search_index_rows:
-            return
-
-        async with db.scoped_session(self.session_maker) as session:
-            # Prepare all insert data with project_id
-            insert_data_list = []
-            for row in search_index_rows:
-                insert_data = row.to_insert()
-                insert_data["project_id"] = self.project_id
-                insert_data_list.append(insert_data)
-
-            # Batch insert all records using executemany
-            await session.execute(
-                text("""
-                    INSERT INTO search_index (
-                        id, title, content_stems, content_snippet, permalink, file_path, type, metadata,
-                        from_id, to_id, relation_type,
-                        entity_id, category,
-                        created_at, updated_at,
-                        project_id
-                    ) VALUES (
-                        :id, :title, :content_stems, :content_snippet, :permalink, :file_path, :type, :metadata,
-                        :from_id, :to_id, :relation_type,
-                        :entity_id, :category,
-                        :created_at, :updated_at,
-                        :project_id
-                    )
-                """),
-                insert_data_list,
-            )
-            logger.debug(f"Bulk indexed {len(search_index_rows)} rows")
-            await session.commit()
-
-    async def delete_by_entity_id(self, entity_id: int):
-        """Delete an item from the search index by entity_id."""
-        async with db.scoped_session(self.session_maker) as session:
-            await session.execute(
-                text(
-                    "DELETE FROM search_index WHERE entity_id = :entity_id AND project_id = :project_id"
-                ),
-                {"entity_id": entity_id, "project_id": self.project_id},
-            )
-            await session.commit()
-
-    async def delete_by_permalink(self, permalink: str):
-        """Delete an item from the search index."""
-        async with db.scoped_session(self.session_maker) as session:
-            await session.execute(
-                text(
-                    "DELETE FROM search_index WHERE permalink = :permalink AND project_id = :project_id"
-                ),
-                {"permalink": permalink, "project_id": self.project_id},
-            )
-            await session.commit()
-
-    async def execute_query(
-        self,
-        query: Executable,
-        params: Dict[str, Any],
-    ) -> Result[Any]:
-        """Execute a query asynchronously."""
-        # logger.debug(f"Executing query: {query}, params: {params}")
-        async with db.scoped_session(self.session_maker) as session:
-            start_time = time.perf_counter()
-            result = await session.execute(query, params)
-            end_time = time.perf_counter()
-            elapsed_time = end_time - start_time
-            logger.debug(f"Query executed successfully in {elapsed_time:.2f}s.")
-            return result
+__all__ = [
+    "SearchRepository",
+    "SearchIndexRow",
+    "create_search_repository",
+]

src/basic_memory/repository/search_repository_base.py

@@ -0,0 +1,240 @@
+"""Abstract base class for search repository implementations."""
+
+from abc import ABC, abstractmethod
+from datetime import datetime
+from typing import Any, Dict, List, Optional
+
+from loguru import logger
+from sqlalchemy import Executable, Result, text
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from basic_memory import db
+from basic_memory.schemas.search import SearchItemType
+from basic_memory.repository.search_index_row import SearchIndexRow
+
+
+class SearchRepositoryBase(ABC):
+    """Abstract base class for backend-specific search repository implementations.
+
+    This class defines the common interface that all search repositories must implement,
+    regardless of whether they use SQLite FTS5 or Postgres tsvector for full-text search.
+
+    Concrete implementations:
+    - SQLiteSearchRepository: Uses FTS5 virtual tables with MATCH queries
+    - PostgresSearchRepository: Uses tsvector/tsquery with GIN indexes
+    """
+
+    def __init__(self, session_maker: async_sessionmaker[AsyncSession], project_id: int):
+        """Initialize with session maker and project_id filter.
+
+        Args:
+            session_maker: SQLAlchemy session maker
+            project_id: Project ID to filter all operations by
+
+        Raises:
+            ValueError: If project_id is None or invalid
+        """
+        if project_id is None or project_id <= 0:  # pragma: no cover
+            raise ValueError("A valid project_id is required for SearchRepository")
+
+        self.session_maker = session_maker
+        self.project_id = project_id
+
+    @abstractmethod
+    async def init_search_index(self) -> None:
+        """Create or recreate the search index.
+
+        Backend-specific implementations:
+        - SQLite: CREATE VIRTUAL TABLE using FTS5
+        - Postgres: CREATE TABLE with tsvector column and GIN indexes
+        """
+        pass
+
+    @abstractmethod
+    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a search term for backend-specific query syntax.
+
+        Args:
+            term: The search term to prepare
+            is_prefix: Whether to add prefix search capability
+
+        Returns:
+            Formatted search term for the backend
+
+        Backend-specific implementations:
+        - SQLite: Quotes FTS5 special characters, adds * wildcards
+        - Postgres: Converts to tsquery syntax with :* prefix operator
+        """
+        pass
+
+    @abstractmethod
+    async def search(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        limit: int = 10,
+        offset: int = 0,
+    ) -> List[SearchIndexRow]:
+        """Search across all indexed content.
+
+        Args:
+            search_text: Full-text search across title and content
+            permalink: Exact permalink match
+            permalink_match: Permalink pattern match (supports *)
+            title: Title search
+            types: Filter by entity types (from metadata.entity_type)
+            after_date: Filter by created_at > after_date
+            search_item_types: Filter by SearchItemType (ENTITY, OBSERVATION, RELATION)
+            limit: Maximum results to return
+            offset: Number of results to skip
+
+        Returns:
+            List of SearchIndexRow results with relevance scores
+
+        Backend-specific implementations:
+        - SQLite: Uses MATCH operator and bm25() for scoring
+        - Postgres: Uses @@ operator and ts_rank() for scoring
+        """
+        pass
+
+    async def index_item(self, search_index_row: SearchIndexRow) -> None:
+        """Index or update a single item.
+
+        This implementation is shared across backends as it uses standard SQL INSERT.
+        """
+
+        async with db.scoped_session(self.session_maker) as session:
+            # Delete existing record if any
+            await session.execute(
+                text(
+                    "DELETE FROM search_index WHERE permalink = :permalink AND project_id = :project_id"
+                ),
+                {"permalink": search_index_row.permalink, "project_id": self.project_id},
+            )
+
+            # When using text() raw SQL, always serialize JSON to string
+            # Both SQLite (TEXT) and Postgres (JSONB) accept JSON strings in raw SQL
+            # The database driver/column type will handle conversion
+            insert_data = search_index_row.to_insert(serialize_json=True)
+            insert_data["project_id"] = self.project_id
+
+            # Insert new record
+            await session.execute(
+                text("""
+                    INSERT INTO search_index (
+                        id, title, content_stems, content_snippet, permalink, file_path, type, metadata,
+                        from_id, to_id, relation_type,
+                        entity_id, category,
+                        created_at, updated_at,
+                        project_id
+                    ) VALUES (
+                        :id, :title, :content_stems, :content_snippet, :permalink, :file_path, :type, :metadata,
+                        :from_id, :to_id, :relation_type,
+                        :entity_id, :category,
+                        :created_at, :updated_at,
+                        :project_id
+                    )
+                """),
+                insert_data,
+            )
+            logger.debug(f"indexed row {search_index_row}")
+            await session.commit()
+
+    async def bulk_index_items(self, search_index_rows: List[SearchIndexRow]) -> None:
+        """Index multiple items in a single batch operation.
+
+        This implementation is shared across backends as it uses standard SQL INSERT.
+
+        Note: This method assumes that any existing records for the entity_id
+        have already been deleted (typically via delete_by_entity_id).
+
+        Args:
+            search_index_rows: List of SearchIndexRow objects to index
+        """
+
+        if not search_index_rows:
+            return
+
+        async with db.scoped_session(self.session_maker) as session:
+            # When using text() raw SQL, always serialize JSON to string
+            # Both SQLite (TEXT) and Postgres (JSONB) accept JSON strings in raw SQL
+            # The database driver/column type will handle conversion
+            insert_data_list = []
+            for row in search_index_rows:
+                insert_data = row.to_insert(serialize_json=True)
+                insert_data["project_id"] = self.project_id
+                insert_data_list.append(insert_data)
+
+            # Batch insert all records using executemany
+            await session.execute(
+                text("""
+                    INSERT INTO search_index (
+                        id, title, content_stems, content_snippet, permalink, file_path, type, metadata,
+                        from_id, to_id, relation_type,
+                        entity_id, category,
+                        created_at, updated_at,
+                        project_id
+                    ) VALUES (
+                        :id, :title, :content_stems, :content_snippet, :permalink, :file_path, :type, :metadata,
+                        :from_id, :to_id, :relation_type,
+                        :entity_id, :category,
+                        :created_at, :updated_at,
+                        :project_id
+                    )
+                """),
+                insert_data_list,
+            )
+            logger.debug(f"Bulk indexed {len(search_index_rows)} rows")
+            await session.commit()
+
+    async def delete_by_entity_id(self, entity_id: int) -> None:
+        """Delete all search index entries for an entity.
+
+        This implementation is shared across backends as it uses standard SQL DELETE.
+        """
+        async with db.scoped_session(self.session_maker) as session:
+            await session.execute(
+                text(
+                    "DELETE FROM search_index WHERE entity_id = :entity_id AND project_id = :project_id"
+                ),
+                {"entity_id": entity_id, "project_id": self.project_id},
+            )
+            await session.commit()
+
+    async def delete_by_permalink(self, permalink: str) -> None:
+        """Delete a search index entry by permalink.
+
+        This implementation is shared across backends as it uses standard SQL DELETE.
+        """
+        async with db.scoped_session(self.session_maker) as session:
+            await session.execute(
+                text(
+                    "DELETE FROM search_index WHERE permalink = :permalink AND project_id = :project_id"
+                ),
+                {"permalink": permalink, "project_id": self.project_id},
+            )
+            await session.commit()
+
+    async def execute_query(
+        self,
+        query: Executable,
+        params: Dict[str, Any],
+    ) -> Result[Any]:
+        """Execute a query asynchronously.
+
+        This implementation is shared across backends for utility query execution.
+        """
+        import time
+
+        async with db.scoped_session(self.session_maker) as session:
+            start_time = time.perf_counter()
+            result = await session.execute(query, params)
+            end_time = time.perf_counter()
+            elapsed_time = end_time - start_time
+            logger.debug(f"Query executed successfully in {elapsed_time:.2f}s.")
+            return result

src/basic_memory/repository/sqlite_search_repository.py

@@ -0,0 +1,438 @@
+"""SQLite FTS5-based search repository implementation."""
+
+import json
+import re
+from datetime import datetime
+from typing import List, Optional
+
+from loguru import logger
+from sqlalchemy import text
+
+from basic_memory import db
+from basic_memory.models.search import CREATE_SEARCH_INDEX
+from basic_memory.repository.search_index_row import SearchIndexRow
+from basic_memory.repository.search_repository_base import SearchRepositoryBase
+from basic_memory.schemas.search import SearchItemType
+
+
+class SQLiteSearchRepository(SearchRepositoryBase):
+    """SQLite FTS5 implementation of search repository.
+
+    Uses SQLite's FTS5 virtual tables for full-text search with:
+    - MATCH operator for queries
+    - bm25() function for relevance scoring
+    - Special character quoting for syntax safety
+    - Prefix wildcard matching with *
+    """
+
+    async def init_search_index(self):
+        """Create FTS5 virtual table for search.
+
+        Note: Drops any existing search_index table first to ensure FTS5 virtual table creation.
+        This is necessary because Base.metadata.create_all() might create a regular table.
+        """
+        logger.info("Initializing SQLite FTS5 search index")
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                # Drop any existing regular or virtual table first
+                await session.execute(text("DROP TABLE IF EXISTS search_index"))
+                # Create FTS5 virtual table
+                await session.execute(CREATE_SEARCH_INDEX)
+                await session.commit()
+        except Exception as e:  # pragma: no cover
+            logger.error(f"Error initializing search index: {e}")
+            raise e
+
+    def _prepare_boolean_query(self, query: str) -> str:
+        """Prepare a Boolean query by quoting individual terms while preserving operators.
+
+        Args:
+            query: A Boolean query like "tier1-test AND unicode" or "(hello OR world) NOT test"
+
+        Returns:
+            A properly formatted Boolean query with quoted terms that need quoting
+        """
+        # Define Boolean operators and their boundaries
+        boolean_pattern = r"(\bAND\b|\bOR\b|\bNOT\b)"
+
+        # Split the query by Boolean operators, keeping the operators
+        parts = re.split(boolean_pattern, query)
+
+        processed_parts = []
+        for part in parts:
+            part = part.strip()
+            if not part:
+                continue
+
+            # If it's a Boolean operator, keep it as is
+            if part in ["AND", "OR", "NOT"]:
+                processed_parts.append(part)
+            else:
+                # Handle parentheses specially - they should be preserved for grouping
+                if "(" in part or ")" in part:
+                    # Parse parenthetical expressions carefully
+                    processed_part = self._prepare_parenthetical_term(part)
+                    processed_parts.append(processed_part)
+                else:
+                    # This is a search term - for Boolean queries, don't add prefix wildcards
+                    prepared_term = self._prepare_single_term(part, is_prefix=False)
+                    processed_parts.append(prepared_term)
+
+        return " ".join(processed_parts)
+
+    def _prepare_parenthetical_term(self, term: str) -> str:
+        """Prepare a term that contains parentheses, preserving the parentheses for grouping.
+
+        Args:
+            term: A term that may contain parentheses like "(hello" or "world)" or "(hello OR world)"
+
+        Returns:
+            A properly formatted term with parentheses preserved
+        """
+        # Handle terms that start/end with parentheses but may contain quotable content
+        result = ""
+        i = 0
+        while i < len(term):
+            if term[i] in "()":
+                # Preserve parentheses as-is
+                result += term[i]
+                i += 1
+            else:
+                # Find the next parenthesis or end of string
+                start = i
+                while i < len(term) and term[i] not in "()":
+                    i += 1
+
+                # Extract the content between parentheses
+                content = term[start:i].strip()
+                if content:
+                    # Only quote if it actually needs quoting (has hyphens, special chars, etc)
+                    # but don't quote if it's just simple words
+                    if self._needs_quoting(content):
+                        escaped_content = content.replace('"', '""')
+                        result += f'"{escaped_content}"'
+                    else:
+                        result += content
+
+        return result
+
+    def _needs_quoting(self, term: str) -> bool:
+        """Check if a term needs to be quoted for FTS5 safety.
+
+        Args:
+            term: The term to check
+
+        Returns:
+            True if the term should be quoted
+        """
+        if not term or not term.strip():
+            return False
+
+        # Characters that indicate we should quote (excluding parentheses which are valid syntax)
+        needs_quoting_chars = [
+            " ",
+            ".",
+            ":",
+            ";",
+            ",",
+            "<",
+            ">",
+            "?",
+            "/",
+            "-",
+            "'",
+            '"',
+            "[",
+            "]",
+            "{",
+            "}",
+            "+",
+            "!",
+            "@",
+            "#",
+            "$",
+            "%",
+            "^",
+            "&",
+            "=",
+            "|",
+            "\\",
+            "~",
+            "`",
+        ]
+
+        return any(c in term for c in needs_quoting_chars)
+
+    def _prepare_single_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a single search term (no Boolean operators).
+
+        Args:
+            term: A single search term
+            is_prefix: Whether to add prefix search capability (* suffix)
+
+        Returns:
+            A properly formatted single term
+        """
+        if not term or not term.strip():
+            return term
+
+        term = term.strip()
+
+        # Check if term is already a proper wildcard pattern (alphanumeric + *)
+        # e.g., "hello*", "test*world" - these should be left alone
+        if "*" in term and all(c.isalnum() or c in "*_-" for c in term):
+            return term
+
+        # Characters that can cause FTS5 syntax errors when used as operators
+        # We're more conservative here - only quote when we detect problematic patterns
+        problematic_chars = [
+            '"',
+            "'",
+            "(",
+            ")",
+            "[",
+            "]",
+            "{",
+            "}",
+            "+",
+            "!",
+            "@",
+            "#",
+            "$",
+            "%",
+            "^",
+            "&",
+            "=",
+            "|",
+            "\\",
+            "~",
+            "`",
+        ]
+
+        # Characters that indicate we should quote (spaces, dots, colons, etc.)
+        # Adding hyphens here because FTS5 can have issues with hyphens followed by wildcards
+        needs_quoting_chars = [" ", ".", ":", ";", ",", "<", ">", "?", "/", "-"]
+
+        # Check if term needs quoting
+        has_problematic = any(c in term for c in problematic_chars)
+        has_spaces_or_special = any(c in term for c in needs_quoting_chars)
+
+        if has_problematic or has_spaces_or_special:
+            # Handle multi-word queries differently from special character queries
+            if " " in term and not any(c in term for c in problematic_chars):
+                # Check if any individual word contains special characters that need quoting
+                words = term.strip().split()
+                has_special_in_words = any(
+                    any(c in word for c in needs_quoting_chars if c != " ") for word in words
+                )
+
+                if not has_special_in_words:
+                    # For multi-word queries with simple words (like "emoji unicode"),
+                    # use boolean AND to handle word order variations
+                    if is_prefix:
+                        # Add prefix wildcard to each word for better matching
+                        prepared_words = [f"{word}*" for word in words if word]
+                    else:
+                        prepared_words = words
+                    term = " AND ".join(prepared_words)
+                else:
+                    # If any word has special characters, quote the entire phrase
+                    escaped_term = term.replace('"', '""')
+                    if is_prefix and not ("/" in term and term.endswith(".md")):
+                        term = f'"{escaped_term}"*'
+                    else:
+                        term = f'"{escaped_term}"'
+            else:
+                # For terms with problematic characters or file paths, use exact phrase matching
+                # Escape any existing quotes by doubling them
+                escaped_term = term.replace('"', '""')
+                # Quote the entire term to handle special characters safely
+                if is_prefix and not ("/" in term and term.endswith(".md")):
+                    # For search terms (not file paths), add prefix matching
+                    term = f'"{escaped_term}"*'
+                else:
+                    # For file paths, use exact matching
+                    term = f'"{escaped_term}"'
+        elif is_prefix:
+            # Only add wildcard for simple terms without special characters
+            term = f"{term}*"
+
+        return term
+
+    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a search term for FTS5 query.
+
+        Args:
+            term: The search term to prepare
+            is_prefix: Whether to add prefix search capability (* suffix)
+
+        For FTS5:
+        - Boolean operators (AND, OR, NOT) are preserved for complex queries
+        - Terms with FTS5 special characters are quoted to prevent syntax errors
+        - Simple terms get prefix wildcards for better matching
+        """
+        # Check for explicit boolean operators - if present, process as Boolean query
+        boolean_operators = [" AND ", " OR ", " NOT "]
+        if any(op in f" {term} " for op in boolean_operators):
+            return self._prepare_boolean_query(term)
+
+        # For non-Boolean queries, use the single term preparation logic
+        return self._prepare_single_term(term, is_prefix)
+
+    async def search(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        limit: int = 10,
+        offset: int = 0,
+    ) -> List[SearchIndexRow]:
+        """Search across all indexed content using SQLite FTS5."""
+        conditions = []
+        params = {}
+        order_by_clause = ""
+
+        # Handle text search for title and content
+        if search_text:
+            # Skip FTS for wildcard-only queries that would cause "unknown special query" errors
+            if search_text.strip() == "*" or search_text.strip() == "":
+                # For wildcard searches, don't add any text conditions - return all results
+                pass
+            else:
+                # Use _prepare_search_term to handle both Boolean and non-Boolean queries
+                processed_text = self._prepare_search_term(search_text.strip())
+                params["text"] = processed_text
+                conditions.append("(title MATCH :text OR content_stems MATCH :text)")
+
+        # Handle title match search
+        if title:
+            title_text = self._prepare_search_term(title.strip(), is_prefix=False)
+            params["title_text"] = title_text
+            conditions.append("title MATCH :title_text")
+
+        # Handle permalink exact search
+        if permalink:
+            params["permalink"] = permalink
+            conditions.append("permalink = :permalink")
+
+        # Handle permalink match search, supports *
+        if permalink_match:
+            # For GLOB patterns, don't use _prepare_search_term as it will quote slashes
+            # GLOB patterns need to preserve their syntax
+            permalink_text = permalink_match.lower().strip()
+            params["permalink"] = permalink_text
+            if "*" in permalink_match:
+                conditions.append("permalink GLOB :permalink")
+            else:
+                # For exact matches without *, we can use FTS5 MATCH
+                # but only prepare the term if it doesn't look like a path
+                if "/" in permalink_text:
+                    conditions.append("permalink = :permalink")
+                else:
+                    permalink_text = self._prepare_search_term(permalink_text, is_prefix=False)
+                    params["permalink"] = permalink_text
+                    conditions.append("permalink MATCH :permalink")
+
+        # Handle entity type filter
+        if search_item_types:
+            type_list = ", ".join(f"'{t.value}'" for t in search_item_types)
+            conditions.append(f"type IN ({type_list})")
+
+        # Handle type filter
+        if types:
+            type_list = ", ".join(f"'{t}'" for t in types)
+            conditions.append(f"json_extract(metadata, '$.entity_type') IN ({type_list})")
+
+        # Handle date filter using datetime() for proper comparison
+        if after_date:
+            params["after_date"] = after_date
+            conditions.append("datetime(created_at) > datetime(:after_date)")
+
+            # order by most recent first
+            order_by_clause = ", updated_at DESC"
+
+        # Always filter by project_id
+        params["project_id"] = self.project_id
+        conditions.append("project_id = :project_id")
+
+        # set limit on search query
+        params["limit"] = limit
+        params["offset"] = offset
+
+        # Build WHERE clause
+        where_clause = " AND ".join(conditions) if conditions else "1=1"
+
+        sql = f"""
+            SELECT
+                project_id,
+                id,
+                title,
+                permalink,
+                file_path,
+                type,
+                metadata,
+                from_id,
+                to_id,
+                relation_type,
+                entity_id,
+                content_snippet,
+                category,
+                created_at,
+                updated_at,
+                bm25(search_index) as score
+            FROM search_index
+            WHERE {where_clause}
+            ORDER BY score ASC {order_by_clause}
+            LIMIT :limit
+            OFFSET :offset
+        """
+
+        logger.trace(f"Search {sql} params: {params}")
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                result = await session.execute(text(sql), params)
+                rows = result.fetchall()
+        except Exception as e:
+            # Handle FTS5 syntax errors and provide user-friendly feedback
+            if "fts5: syntax error" in str(e).lower():  # pragma: no cover
+                logger.warning(f"FTS5 syntax error for search term: {search_text}, error: {e}")
+                # Return empty results rather than crashing
+                return []
+            else:
+                # Re-raise other database errors
+                logger.error(f"Database error during search: {e}")
+                raise
+
+        results = [
+            SearchIndexRow(
+                project_id=self.project_id,
+                id=row.id,
+                title=row.title,
+                permalink=row.permalink,
+                file_path=row.file_path,
+                type=row.type,
+                score=row.score,
+                metadata=json.loads(row.metadata) if row.metadata else {},
+                from_id=row.from_id,
+                to_id=row.to_id,
+                relation_type=row.relation_type,
+                entity_id=row.entity_id,
+                content_snippet=row.content_snippet,
+                category=row.category,
+                created_at=row.created_at,
+                updated_at=row.updated_at,
+            )
+            for row in rows
+        ]
+
+        logger.trace(f"Found {len(results)} search results")
+        for r in results:
+            logger.trace(
+                f"Search result: project_id: {r.project_id} type:{r.type} title: {r.title} permalink: {r.permalink} score: {r.score}"
+            )
+
+        return results

src/basic_memory/schemas/base.py

@@ -21,13 +21,38 @@ from typing import List, Optional, Annotated, Dict
 from annotated_types import MinLen, MaxLen
 from dateparser import parse
 
-from pydantic import BaseModel, BeforeValidator, Field, model_validator
+from pydantic import BaseModel, BeforeValidator, Field, model_validator, computed_field
 
 from basic_memory.config import ConfigManager
 from basic_memory.file_utils import sanitize_for_filename, sanitize_for_folder
 from basic_memory.utils import generate_permalink
 
 
+def has_valid_file_extension(filename: str) -> bool:
+    """Check if a filename has a valid file extension recognized by mimetypes.
+
+    This is used to determine whether to split the extension when processing
+    titles in kebab_filenames mode. Prevents treating periods in version numbers
+    or decimals as file extensions.
+
+    Args:
+        filename: The filename to check
+
+    Returns:
+        True if the filename has a recognized file extension, False otherwise
+
+    Examples:
+        >>> has_valid_file_extension("document.md")
+        True
+        >>> has_valid_file_extension("Version 2.0.0")
+        False
+        >>> has_valid_file_extension("image.png")
+        True
+    """
+    mime_type, _ = mimetypes.guess_type(filename)
+    return mime_type is not None
+
+
 def to_snake_case(name: str) -> str:
     """Convert a string to snake_case.
 
@@ -232,12 +257,17 @@ class Entity(BaseModel):
         use_kebab_case = app_config.kebab_filenames
 
         if use_kebab_case:
-            fixed_title = generate_permalink(file_path=fixed_title, split_extension=False)
+            # Convert to kebab-case: lowercase with hyphens, preserving periods in version numbers
+            # generate_permalink() uses mimetypes to detect real file extensions and only splits
+            # them off, avoiding misinterpreting periods in version numbers as extensions
+            has_extension = has_valid_file_extension(fixed_title)
+            fixed_title = generate_permalink(file_path=fixed_title, split_extension=has_extension)
 
         return fixed_title
 
+    @computed_field
     @property
-    def file_path(self):
+    def file_path(self) -> str:
         """Get the file path for this entity based on its permalink."""
         safe_title = self.safe_title
         if self.content_type == "text/markdown":

src/basic_memory/schemas/cloud.py

@@ -41,6 +41,10 @@ class CloudProjectCreateRequest(BaseModel):
 class CloudProjectCreateResponse(BaseModel):
     """Response from creating a cloud project."""
 
-    name: str = Field(..., description="Created project name")
-    path: str = Field(..., description="Created project path")
-    message: str = Field(default="", description="Success message")
+    message: str = Field(..., description="Status message about the project creation")
+    status: str = Field(..., description="Status of the creation (success or error)")
+    default: bool = Field(..., description="True if the project was set as the default")
+    old_project: dict | None = Field(None, description="Information about the previous project")
+    new_project: dict | None = Field(
+        None, description="Information about the newly created project"
+    )

src/basic_memory/schemas/sync_report.py

@@ -1,6 +1,7 @@
 """Pydantic schemas for sync report responses."""
 
-from typing import TYPE_CHECKING, Dict, Set
+from datetime import datetime
+from typing import TYPE_CHECKING, Dict, List, Set
 
 from pydantic import BaseModel, Field
 
@@ -9,6 +10,17 @@ if TYPE_CHECKING:
     from basic_memory.sync.sync_service import SyncReport
 
 
+class SkippedFileResponse(BaseModel):
+    """Information about a file that was skipped due to repeated failures."""
+
+    path: str = Field(description="File path relative to project root")
+    reason: str = Field(description="Error message from last failure")
+    failure_count: int = Field(description="Number of consecutive failures")
+    first_failed: datetime = Field(description="Timestamp of first failure")
+
+    model_config = {"from_attributes": True}
+
+
 class SyncReportResponse(BaseModel):
     """Report of file changes found compared to database state.
 
@@ -24,6 +36,9 @@ class SyncReportResponse(BaseModel):
     checksums: Dict[str, str] = Field(
         default_factory=dict, description="Current file checksums (path -> checksum)"
     )
+    skipped_files: List[SkippedFileResponse] = Field(
+        default_factory=list, description="Files skipped due to repeated failures"
+    )
     total: int = Field(description="Total number of changes")
 
     @classmethod
@@ -42,6 +57,15 @@ class SyncReportResponse(BaseModel):
             deleted=report.deleted,
             moves=report.moves,
             checksums=report.checksums,
+            skipped_files=[
+                SkippedFileResponse(
+                    path=skipped.path,
+                    reason=skipped.reason,
+                    failure_count=skipped.failure_count,
+                    first_failed=skipped.first_failed,
+                )
+                for skipped in report.skipped_files
+            ],
             total=report.total,
         )
 

src/basic_memory/services/context_service.py

@@ -9,6 +9,7 @@ from sqlalchemy import text
 
 from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.repository.observation_repository import ObservationRepository
+from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
 from basic_memory.repository.search_repository import SearchRepository, SearchIndexRow
 from basic_memory.schemas.memory import MemoryUrl, memory_url_path
 from basic_memory.schemas.search import SearchItemType
@@ -252,9 +253,6 @@ class ContextService:
         # Build the VALUES clause for entity IDs
         entity_id_values = ", ".join([str(i) for i in entity_ids])
 
-        # For compatibility with the old query, we still need this for filtering
-        values = ", ".join([f"('{t}', {i})" for t, i in type_id_pairs])
-
         # Parameters for bindings - include project_id for security filtering
         params = {
             "max_depth": max_depth,
@@ -264,7 +262,14 @@ class ContextService:
 
         # Build date and timeframe filters conditionally based on since parameter
         if since:
-            params["since_date"] = since.isoformat()  # pyright: ignore
+            # SQLite accepts ISO strings, but Postgres/asyncpg requires datetime objects
+            if isinstance(self.search_repository, PostgresSearchRepository):
+                # asyncpg expects timezone-NAIVE datetime in UTC for DateTime(timezone=True) columns
+                # even though the column stores timezone-aware values
+                since_utc = since.astimezone(timezone.utc) if since.tzinfo else since
+                params["since_date"] = since_utc.replace(tzinfo=None)  # pyright: ignore
+            else:
+                params["since_date"] = since.isoformat()  # pyright: ignore
             date_filter = "AND e.created_at >= :since_date"
             relation_date_filter = "AND e_from.created_at >= :since_date"
             timeframe_condition = "AND eg.relation_date >= :since_date"
@@ -279,13 +284,210 @@ class ContextService:
 
         # Use a CTE that operates directly on entity and relation tables
         # This avoids the overhead of the search_index virtual table
-        query = text(f"""
+        # Note: Postgres and SQLite have different CTE limitations:
+        # - Postgres: doesn't allow multiple UNION ALL branches referencing the CTE
+        # - SQLite: doesn't support LATERAL joins
+        # So we need different queries for each database backend
+
+        # Detect database backend
+        is_postgres = isinstance(self.search_repository, PostgresSearchRepository)
+
+        if is_postgres:
+            query = self._build_postgres_query(
+                entity_id_values,
+                date_filter,
+                project_filter,
+                relation_date_filter,
+                relation_project_filter,
+                timeframe_condition,
+            )
+        else:
+            # SQLite needs VALUES clause for exclusion (not needed for Postgres)
+            values = ", ".join([f"('{t}', {i})" for t, i in type_id_pairs])
+            query = self._build_sqlite_query(
+                entity_id_values,
+                date_filter,
+                project_filter,
+                relation_date_filter,
+                relation_project_filter,
+                timeframe_condition,
+                values,
+            )
+
+        result = await self.search_repository.execute_query(query, params=params)
+        rows = result.all()
+
+        context_rows = [
+            ContextResultRow(
+                type=row.type,
+                id=row.id,
+                title=row.title,
+                permalink=row.permalink,
+                file_path=row.file_path,
+                from_id=row.from_id,
+                to_id=row.to_id,
+                relation_type=row.relation_type,
+                content=row.content,
+                category=row.category,
+                entity_id=row.entity_id,
+                depth=row.depth,
+                root_id=row.root_id,
+                created_at=row.created_at,
+            )
+            for row in rows
+        ]
+        return context_rows
+
+    def _build_postgres_query(
+        self,
+        entity_id_values: str,
+        date_filter: str,
+        project_filter: str,
+        relation_date_filter: str,
+        relation_project_filter: str,
+        timeframe_condition: str,
+    ):
+        """Build Postgres-specific CTE query using LATERAL joins."""
+        return text(f"""
         WITH RECURSIVE entity_graph AS (
             -- Base case: seed entities
-            SELECT 
+            SELECT
                 e.id,
                 'entity' as type,
-                e.title, 
+                e.title,
+                e.permalink,
+                e.file_path,
+                CAST(NULL AS INTEGER) as from_id,
+                CAST(NULL AS INTEGER) as to_id,
+                CAST(NULL AS TEXT) as relation_type,
+                CAST(NULL AS TEXT) as content,
+                CAST(NULL AS TEXT) as category,
+                CAST(NULL AS INTEGER) as entity_id,
+                0 as depth,
+                e.id as root_id,
+                e.created_at,
+                e.created_at as relation_date
+            FROM entity e
+            WHERE e.id IN ({entity_id_values})
+            {date_filter}
+            {project_filter}
+
+            UNION ALL
+
+            -- Fetch BOTH relations AND connected entities in a single recursive step
+            -- Postgres only allows ONE reference to the recursive CTE in the recursive term
+            -- We use CROSS JOIN LATERAL to generate two rows (relation + entity) from each traversal
+            SELECT
+                CASE
+                    WHEN step_type = 1 THEN r.id
+                    ELSE e.id
+                END as id,
+                CASE
+                    WHEN step_type = 1 THEN 'relation'
+                    ELSE 'entity'
+                END as type,
+                CASE
+                    WHEN step_type = 1 THEN r.relation_type || ': ' || r.to_name
+                    ELSE e.title
+                END as title,
+                CASE
+                    WHEN step_type = 1 THEN ''
+                    ELSE COALESCE(e.permalink, '')
+                END as permalink,
+                CASE
+                    WHEN step_type = 1 THEN e_from.file_path
+                    ELSE e.file_path
+                END as file_path,
+                CASE
+                    WHEN step_type = 1 THEN r.from_id
+                    ELSE NULL
+                END as from_id,
+                CASE
+                    WHEN step_type = 1 THEN r.to_id
+                    ELSE NULL
+                END as to_id,
+                CASE
+                    WHEN step_type = 1 THEN r.relation_type
+                    ELSE NULL
+                END as relation_type,
+                CAST(NULL AS TEXT) as content,
+                CAST(NULL AS TEXT) as category,
+                CAST(NULL AS INTEGER) as entity_id,
+                eg.depth + step_type as depth,
+                eg.root_id,
+                CASE
+                    WHEN step_type = 1 THEN e_from.created_at
+                    ELSE e.created_at
+                END as created_at,
+                CASE
+                    WHEN step_type = 1 THEN e_from.created_at
+                    ELSE eg.relation_date
+                END as relation_date
+            FROM entity_graph eg
+            CROSS JOIN LATERAL (VALUES (1), (2)) AS steps(step_type)
+            JOIN relation r ON (
+                eg.type = 'entity' AND
+                (r.from_id = eg.id OR r.to_id = eg.id)
+            )
+            JOIN entity e_from ON (
+                r.from_id = e_from.id
+                {relation_project_filter}
+            )
+            LEFT JOIN entity e ON (
+                step_type = 2 AND
+                e.id = CASE
+                    WHEN r.from_id = eg.id THEN r.to_id
+                    ELSE r.from_id
+                END
+                {date_filter}
+                {project_filter}
+            )
+            WHERE eg.depth < :max_depth
+            AND (step_type = 1 OR (step_type = 2 AND e.id IS NOT NULL AND e.id != eg.id))
+            {timeframe_condition}
+        )
+        -- Materialize and filter
+        SELECT DISTINCT
+            type,
+            id,
+            title,
+            permalink,
+            file_path,
+            from_id,
+            to_id,
+            relation_type,
+            content,
+            category,
+            entity_id,
+            MIN(depth) as depth,
+            root_id,
+            created_at
+        FROM entity_graph
+        WHERE depth > 0
+        GROUP BY type, id, title, permalink, file_path, from_id, to_id,
+                 relation_type, content, category, entity_id, root_id, created_at
+        ORDER BY depth, type, id
+        LIMIT :max_results
+       """)
+
+    def _build_sqlite_query(
+        self,
+        entity_id_values: str,
+        date_filter: str,
+        project_filter: str,
+        relation_date_filter: str,
+        relation_project_filter: str,
+        timeframe_condition: str,
+        values: str,
+    ):
+        """Build SQLite-specific CTE query using multiple UNION ALL branches."""
+        return text(f"""
+        WITH RECURSIVE entity_graph AS (
+            -- Base case: seed entities
+            SELECT
+                e.id,
+                'entity' as type,
+                e.title,
                 e.permalink,
                 e.file_path,
                 NULL as from_id,
@@ -311,7 +513,6 @@ class ContextService:
                 r.id,
                 'relation' as type,
                 r.relation_type || ': ' || r.to_name as title,
-                -- Relation model doesn't have permalink column - we'll generate it at runtime
                 '' as permalink,
                 e_from.file_path,
                 r.from_id,
@@ -322,7 +523,7 @@ class ContextService:
                 NULL as entity_id,
                 eg.depth + 1,
                 eg.root_id,
-                e_from.created_at, -- Use the from_entity's created_at since relation has no timestamp
+                e_from.created_at,
                 e_from.created_at as relation_date,
                 CASE WHEN r.from_id = eg.id THEN 0 ELSE 1 END as is_incoming
             FROM entity_graph eg
@@ -337,7 +538,6 @@ class ContextService:
             )
             LEFT JOIN entity e_to ON (r.to_id = e_to.id)
             WHERE eg.depth < :max_depth
-            -- Ensure to_entity (if exists) also belongs to same project
             AND (r.to_id IS NULL OR e_to.project_id = :project_id)
 
             UNION ALL
@@ -347,9 +547,9 @@ class ContextService:
                 e.id,
                 'entity' as type,
                 e.title,
-                CASE 
-                    WHEN e.permalink IS NULL THEN '' 
-                    ELSE e.permalink 
+                CASE
+                    WHEN e.permalink IS NULL THEN ''
+                    ELSE e.permalink
                 END as permalink,
                 e.file_path,
                 NULL as from_id,
@@ -366,7 +566,7 @@ class ContextService:
             FROM entity_graph eg
             JOIN entity e ON (
                 eg.type = 'relation' AND
-                e.id = CASE 
+                e.id = CASE
                     WHEN eg.is_incoming = 0 THEN eg.to_id
                     ELSE eg.from_id
                 END
@@ -374,10 +574,9 @@ class ContextService:
                 {project_filter}
             )
             WHERE eg.depth < :max_depth
-            -- Only include entities connected by relations within timeframe if specified
             {timeframe_condition}
         )
-        SELECT DISTINCT 
+        SELECT DISTINCT
             type,
             id,
             title,
@@ -393,33 +592,9 @@ class ContextService:
             root_id,
             created_at
         FROM entity_graph
-        WHERE (type, id) NOT IN ({values})
-        GROUP BY
-            type, id
+        WHERE depth > 0
+        GROUP BY type, id, title, permalink, file_path, from_id, to_id,
+                 relation_type, content, category, entity_id, root_id, created_at
         ORDER BY depth, type, id
         LIMIT :max_results
        """)
-
-        result = await self.search_repository.execute_query(query, params=params)
-        rows = result.all()
-
-        context_rows = [
-            ContextResultRow(
-                type=row.type,
-                id=row.id,
-                title=row.title,
-                permalink=row.permalink,
-                file_path=row.file_path,
-                from_id=row.from_id,
-                to_id=row.to_id,
-                relation_type=row.relation_type,
-                content=row.content,
-                category=row.category,
-                entity_id=row.entity_id,
-                depth=row.depth,
-                root_id=row.root_id,
-                created_at=row.created_at,
-            )
-            for row in rows
-        ]
-        return context_rows

src/basic_memory/services/entity_service.py

@@ -623,7 +623,7 @@ class EntityService(BaseService[EntityModel]):
         Args:
             current_content: The current markdown content
             section_header: The section header to find and replace (e.g., "## Section Name")
-            new_content: The new content to replace the section with
+            new_content: The new content to replace the section with (should not include the header itself)
 
         Returns:
             The updated content with the section replaced
@@ -635,6 +635,13 @@ class EntityService(BaseService[EntityModel]):
         if not section_header.startswith("#"):
             section_header = "## " + section_header
 
+        # Strip duplicate header from new_content if present (fix for issue #390)
+        # LLMs sometimes include the section header in their content, which would create duplicates
+        new_content_lines = new_content.lstrip().split("\n")
+        if new_content_lines and new_content_lines[0].strip() == section_header.strip():
+            # Remove the duplicate header line
+            new_content = "\n".join(new_content_lines[1:]).lstrip()
+
         # First pass: count matching sections to check for duplicates
         lines = current_content.split("\n")
         matching_sections = []

src/basic_memory/services/exceptions.py

@@ -20,3 +20,18 @@ class DirectoryOperationError(Exception):
     """Raised when directory operations fail"""
 
     pass
+
+
+class SyncFatalError(Exception):
+    """Raised when sync encounters a fatal error that prevents continuation.
+
+    Fatal errors include:
+    - Project deleted during sync (FOREIGN KEY constraint)
+    - Database corruption
+    - Critical system failures
+
+    When this exception is raised, the entire sync operation should be terminated
+    immediately rather than attempting to continue with remaining files.
+    """
+
+    pass

src/basic_memory/services/file_service.py

@@ -1,12 +1,17 @@
 """Service for file operations with checksum tracking."""
 
+import asyncio
+import hashlib
 import mimetypes
 from os import stat_result
 from pathlib import Path
 from typing import Any, Dict, Tuple, Union
 
+import aiofiles
+import yaml
+
 from basic_memory import file_utils
-from basic_memory.file_utils import FileError
+from basic_memory.file_utils import FileError, ParseError
 from basic_memory.markdown.markdown_processor import MarkdownProcessor
 from basic_memory.models import Entity as EntityModel
 from basic_memory.schemas import Entity as EntitySchema
@@ -16,13 +21,15 @@ from loguru import logger
 
 
 class FileService:
-    """Service for handling file operations.
+    """Service for handling file operations with concurrency control.
 
     All paths are handled as Path objects internally. Strings are converted to
     Path objects when passed in. Relative paths are assumed to be relative to
     base_path.
 
     Features:
+    - True async I/O with aiofiles (non-blocking)
+    - Built-in concurrency limits (semaphore)
     - Consistent file writing with checksums
     - Frontmatter management
     - Atomic operations
@@ -33,9 +40,13 @@ class FileService:
         self,
         base_path: Path,
         markdown_processor: MarkdownProcessor,
+        max_concurrent_files: int = 10,
     ):
         self.base_path = base_path.resolve()  # Get absolute path
         self.markdown_processor = markdown_processor
+        # Semaphore to limit concurrent file operations
+        # Prevents OOM on large projects by processing files in batches
+        self._file_semaphore = asyncio.Semaphore(max_concurrent_files)
 
     def get_entity_path(self, entity: Union[EntityModel, EntitySchema]) -> Path:
         """Generate absolute filesystem path for entity.
@@ -104,6 +115,33 @@ class FileService:
             logger.error("Failed to check file existence", path=str(path), error=str(e))
             raise FileOperationError(f"Failed to check file existence: {e}")
 
+    async def ensure_directory(self, path: FilePath) -> None:
+        """Ensure directory exists, creating if necessary.
+
+        Uses semaphore to control concurrency for directory creation operations.
+
+        Args:
+            path: Directory path to ensure (Path or string)
+
+        Raises:
+            FileOperationError: If directory creation fails
+        """
+        try:
+            # Convert string to Path if needed
+            path_obj = self.base_path / path if isinstance(path, str) else path
+            full_path = path_obj if path_obj.is_absolute() else self.base_path / path_obj
+
+            # Use semaphore for concurrency control
+            async with self._file_semaphore:
+                # Run blocking mkdir in thread pool
+                loop = asyncio.get_event_loop()
+                await loop.run_in_executor(
+                    None, lambda: full_path.mkdir(parents=True, exist_ok=True)
+                )
+        except Exception as e:  # pragma: no cover
+            logger.error("Failed to create directory", path=str(path), error=str(e))
+            raise FileOperationError(f"Failed to create directory {path}: {e}")
+
     async def write_file(self, path: FilePath, content: str) -> str:
         """Write content to file and return checksum.
 
@@ -126,7 +164,7 @@ class FileService:
 
         try:
             # Ensure parent directory exists
-            await file_utils.ensure_directory(full_path.parent)
+            await self.ensure_directory(full_path.parent)
 
             # Write content atomically
             logger.info(
@@ -147,9 +185,45 @@ class FileService:
             logger.exception("File write error", path=str(full_path), error=str(e))
             raise FileOperationError(f"Failed to write file: {e}")
 
-    # TODO remove read_file
+    async def read_file_content(self, path: FilePath) -> str:
+        """Read file content using true async I/O with aiofiles.
+
+        Handles both absolute and relative paths. Relative paths are resolved
+        against base_path.
+
+        Args:
+            path: Path to read (Path or string)
+
+        Returns:
+            File content as string
+
+        Raises:
+            FileOperationError: If read fails
+        """
+        # Convert string to Path if needed
+        path_obj = self.base_path / path if isinstance(path, str) else path
+        full_path = path_obj if path_obj.is_absolute() else self.base_path / path_obj
+
+        try:
+            logger.debug("Reading file content", operation="read_file_content", path=str(full_path))
+            async with aiofiles.open(full_path, mode="r", encoding="utf-8") as f:
+                content = await f.read()
+
+            logger.debug(
+                "File read completed",
+                path=str(full_path),
+                content_length=len(content),
+            )
+            return content
+
+        except Exception as e:
+            logger.exception("File read error", path=str(full_path), error=str(e))
+            raise FileOperationError(f"Failed to read file: {e}")
+
     async def read_file(self, path: FilePath) -> Tuple[str, str]:
-        """Read file and compute checksum.
+        """Read file and compute checksum using true async I/O.
+
+        Uses aiofiles for non-blocking file reads.
 
         Handles both absolute and relative paths. Relative paths are resolved
         against base_path.
@@ -169,7 +243,11 @@ class FileService:
 
         try:
             logger.debug("Reading file", operation="read_file", path=str(full_path))
-            content = full_path.read_text(encoding="utf-8")
+
+            # Use aiofiles for non-blocking read
+            async with aiofiles.open(full_path, mode="r", encoding="utf-8") as f:
+                content = await f.read()
+
             checksum = await file_utils.compute_checksum(content)
 
             logger.debug(
@@ -199,29 +277,85 @@ class FileService:
         full_path.unlink(missing_ok=True)
 
     async def update_frontmatter(self, path: FilePath, updates: Dict[str, Any]) -> str:
-        """
-        Update frontmatter fields in a file while preserving all content.
+        """Update frontmatter fields in a file while preserving all content.
+
+        Only modifies the frontmatter section, leaving all content untouched.
+        Creates frontmatter section if none exists.
+        Returns checksum of updated file.
+
+        Uses aiofiles for true async I/O (non-blocking).
 
         Args:
-            path: Path to the file (Path or string)
-            updates: Dictionary of frontmatter fields to update
+            path: Path to markdown file (Path or string)
+            updates: Dict of frontmatter fields to update
 
         Returns:
             Checksum of updated file
+
+        Raises:
+            FileOperationError: If file operations fail
+            ParseError: If frontmatter parsing fails
         """
         # Convert string to Path if needed
         path_obj = self.base_path / path if isinstance(path, str) else path
         full_path = path_obj if path_obj.is_absolute() else self.base_path / path_obj
-        return await file_utils.update_frontmatter(full_path, updates)
+
+        try:
+            # Read current content using aiofiles
+            async with aiofiles.open(full_path, mode="r", encoding="utf-8") as f:
+                content = await f.read()
+
+            # Parse current frontmatter with proper error handling for malformed YAML
+            current_fm = {}
+            if file_utils.has_frontmatter(content):
+                try:
+                    current_fm = file_utils.parse_frontmatter(content)
+                    content = file_utils.remove_frontmatter(content)
+                except (ParseError, yaml.YAMLError) as e:
+                    # Log warning and treat as plain markdown without frontmatter
+                    logger.warning(
+                        f"Failed to parse YAML frontmatter in {full_path}: {e}. "
+                        "Treating file as plain markdown without frontmatter."
+                    )
+                    # Keep full content, treat as having no frontmatter
+                    current_fm = {}
+
+            # Update frontmatter
+            new_fm = {**current_fm, **updates}
+
+            # Write new file with updated frontmatter
+            yaml_fm = yaml.dump(new_fm, sort_keys=False, allow_unicode=True)
+            final_content = f"---\n{yaml_fm}---\n\n{content.strip()}"
+
+            logger.debug(
+                "Updating frontmatter", path=str(full_path), update_keys=list(updates.keys())
+            )
+
+            await file_utils.write_file_atomic(full_path, final_content)
+            return await file_utils.compute_checksum(final_content)
+
+        except Exception as e:
+            # Only log real errors (not YAML parsing, which is handled above)
+            if not isinstance(e, (ParseError, yaml.YAMLError)):
+                logger.error(
+                    "Failed to update frontmatter",
+                    path=str(full_path),
+                    error=str(e),
+                )
+            raise FileOperationError(f"Failed to update frontmatter: {e}")
 
     async def compute_checksum(self, path: FilePath) -> str:
-        """Compute checksum for a file.
+        """Compute checksum for a file using true async I/O.
+
+        Uses aiofiles for non-blocking I/O with 64KB chunked reading.
+        Semaphore limits concurrent file operations to prevent OOM.
+        Memory usage is constant regardless of file size.
 
         Args:
             path: Path to the file (Path or string)
 
         Returns:
-            Checksum of the file content
+            SHA256 checksum hex string
 
         Raises:
             FileError: If checksum computation fails
@@ -230,18 +364,22 @@ class FileService:
         path_obj = self.base_path / path if isinstance(path, str) else path
         full_path = path_obj if path_obj.is_absolute() else self.base_path / path_obj
 
-        try:
-            if self.is_markdown(path):
-                # read str
-                content = full_path.read_text(encoding="utf-8")
-            else:
-                # read bytes
-                content = full_path.read_bytes()
-            return await file_utils.compute_checksum(content)
+        # Semaphore controls concurrency - max N files processed at once
+        async with self._file_semaphore:
+            try:
+                hasher = hashlib.sha256()
+                chunk_size = 65536  # 64KB chunks
 
-        except Exception as e:  # pragma: no cover
-            logger.error("Failed to compute checksum", path=str(full_path), error=str(e))
-            raise FileError(f"Failed to compute checksum for {path}: {e}")
+                # async I/O with aiofiles
+                async with aiofiles.open(full_path, mode="rb") as f:
+                    while chunk := await f.read(chunk_size):
+                        hasher.update(chunk)
+
+                return hasher.hexdigest()
+
+            except Exception as e:  # pragma: no cover
+                logger.error("Failed to compute checksum", path=str(full_path), error=str(e))
+                raise FileError(f"Failed to compute checksum for {path}: {e}")
 
     def file_stats(self, path: FilePath) -> stat_result:
         """Return file stats for a given path.

src/basic_memory/services/initialization.py

@@ -118,18 +118,8 @@ async def initialize_file_sync(
             sync_dir = Path(project.path)
             await sync_service.sync(sync_dir, project_name=project.name)
             logger.info(f"Background sync completed successfully for project: {project.name}")
-
-            # Mark project as watching for changes after successful sync
-            from basic_memory.services.sync_status_service import sync_status_tracker
-
-            sync_status_tracker.start_project_watch(project.name)
-            logger.info(f"Project {project.name} is now watching for changes")
         except Exception as e:  # pragma: no cover
             logger.error(f"Error in background sync for project {project.name}: {e}")
-            # Mark sync as failed for this project
-            from basic_memory.services.sync_status_service import sync_status_tracker
-
-            sync_status_tracker.fail_project_sync(project.name, str(e))
 
     # Create background tasks for all project syncs (non-blocking)
     sync_tasks = [

src/basic_memory/services/project_service.py

@@ -1,7 +1,9 @@
 """Project management service for Basic Memory."""
 
+import asyncio
 import json
 import os
+import shutil
 from datetime import datetime
 from pathlib import Path
 from typing import Dict, Optional, Sequence
@@ -219,11 +221,12 @@ class ProjectService:
 
         logger.info(f"Project '{name}' added at {resolved_path}")
 
-    async def remove_project(self, name: str) -> None:
+    async def remove_project(self, name: str, delete_notes: bool = False) -> None:
         """Remove a project from configuration and database.
 
         Args:
             name: The name of the project to remove
+            delete_notes: If True, delete the project directory from filesystem
 
         Raises:
             ValueError: If the project doesn't exist or is the default project
@@ -231,16 +234,43 @@ class ProjectService:
         if not self.repository:  # pragma: no cover
             raise ValueError("Repository is required for remove_project")
 
-        # First remove from config (this will validate the project exists and is not default)
-        self.config_manager.remove_project(name)
-
-        # Then remove from database using robust lookup
+        # Get project from database first
         project = await self.get_project(name)
-        if project:
-            await self.repository.delete(project.id)
+        if not project:
+            raise ValueError(f"Project '{name}' not found")
+
+        project_path = project.path
+
+        # Check if project is default (in cloud mode, check database; in local mode, check config)
+        if project.is_default or name == self.config_manager.config.default_project:
+            raise ValueError(f"Cannot remove the default project '{name}'")
+
+        # Remove from config if it exists there (may not exist in cloud mode)
+        try:
+            self.config_manager.remove_project(name)
+        except ValueError:
+            # Project not in config - that's OK in cloud mode, continue with database deletion
+            logger.debug(f"Project '{name}' not found in config, removing from database only")
+
+        # Remove from database
+        await self.repository.delete(project.id)
 
         logger.info(f"Project '{name}' removed from configuration and database")
 
+        # Optionally delete the project directory
+        if delete_notes and project_path:
+            try:
+                path_obj = Path(project_path)
+                if path_obj.exists() and path_obj.is_dir():
+                    await asyncio.to_thread(shutil.rmtree, project_path)
+                    logger.info(f"Deleted project directory: {project_path}")
+                else:
+                    logger.warning(
+                        f"Project directory not found or not a directory: {project_path}"
+                    )
+            except Exception as e:
+                logger.warning(f"Failed to delete project directory {project_path}: {e}")
+
     async def set_default_project(self, name: str) -> None:
         """Set the default project in configuration and database.
 
@@ -360,11 +390,15 @@ class ProjectService:
                 }
                 await self.repository.create(project_data)
 
-        # Add projects that exist in DB but not in config to config
+        # Remove projects that exist in DB but not in config
+        # Config is the source of truth - if a project was deleted from config,
+        # it should be deleted from DB too (fixes issue #193)
         for name, project in db_projects_by_permalink.items():
             if name not in config_projects:
-                logger.info(f"Adding project '{name}' to configuration")
-                self.config_manager.add_project(name, project.path)
+                logger.info(
+                    f"Removing project '{name}' from database (deleted from config, source of truth)"
+                )
+                await self.repository.delete(project.id)
 
         # Ensure database default project state is consistent
         await self._ensure_single_default_project()
@@ -732,25 +766,42 @@ class ProjectService:
         )
 
         # Query for monthly entity creation (project filtered)
+        # Use different date formatting for SQLite vs Postgres
+        from basic_memory.config import DatabaseBackend
+
+        is_postgres = self.config_manager.config.database_backend == DatabaseBackend.POSTGRES
+        date_format = (
+            "to_char(created_at, 'YYYY-MM')" if is_postgres else "strftime('%Y-%m', created_at)"
+        )
+
+        # Postgres needs datetime objects, SQLite needs ISO strings
+        six_months_param = six_months_ago if is_postgres else six_months_ago.isoformat()
+
         entity_growth_result = await self.repository.execute_query(
-            text("""
-            SELECT 
-                strftime('%Y-%m', created_at) AS month,
+            text(f"""
+            SELECT
+                {date_format} AS month,
                 COUNT(*) AS count
             FROM entity
             WHERE created_at >= :six_months_ago AND project_id = :project_id
             GROUP BY month
             ORDER BY month
         """),
-            {"six_months_ago": six_months_ago.isoformat(), "project_id": project_id},
+            {"six_months_ago": six_months_param, "project_id": project_id},
         )
         entity_growth = {row[0]: row[1] for row in entity_growth_result.fetchall()}
 
         # Query for monthly observation creation (project filtered)
+        date_format_entity = (
+            "to_char(entity.created_at, 'YYYY-MM')"
+            if is_postgres
+            else "strftime('%Y-%m', entity.created_at)"
+        )
+
         observation_growth_result = await self.repository.execute_query(
-            text("""
-            SELECT 
-                strftime('%Y-%m', entity.created_at) AS month,
+            text(f"""
+            SELECT
+                {date_format_entity} AS month,
                 COUNT(*) AS count
             FROM observation
             INNER JOIN entity ON observation.entity_id = entity.id
@@ -758,15 +809,15 @@ class ProjectService:
             GROUP BY month
             ORDER BY month
         """),
-            {"six_months_ago": six_months_ago.isoformat(), "project_id": project_id},
+            {"six_months_ago": six_months_param, "project_id": project_id},
         )
         observation_growth = {row[0]: row[1] for row in observation_growth_result.fetchall()}
 
         # Query for monthly relation creation (project filtered)
         relation_growth_result = await self.repository.execute_query(
-            text("""
-            SELECT 
-                strftime('%Y-%m', entity.created_at) AS month,
+            text(f"""
+            SELECT
+                {date_format_entity} AS month,
                 COUNT(*) AS count
             FROM relation
             INNER JOIN entity ON relation.from_id = entity.id
@@ -774,7 +825,7 @@ class ProjectService:
             GROUP BY month
             ORDER BY month
         """),
-            {"six_months_ago": six_months_ago.isoformat(), "project_id": project_id},
+            {"six_months_ago": six_months_param, "project_id": project_id},
         )
         relation_growth = {row[0]: row[1] for row in relation_growth_result.fetchall()}
 

src/basic_memory/services/search_service.py

@@ -185,6 +185,7 @@ class SearchService:
                 entity_id=entity.id,
                 type=SearchItemType.ENTITY.value,
                 title=entity.title,
+                permalink=entity.permalink,  # Required for Postgres NOT NULL constraint
                 file_path=entity.file_path,
                 metadata={
                     "entity_type": entity.entity_type,

src/basic_memory/services/sync_status_service.py

@@ -1,198 +0,0 @@
-"""Simple sync status tracking service."""
-
-from dataclasses import dataclass
-from enum import Enum
-from typing import Dict, Optional
-
-
-class SyncStatus(Enum):
-    """Status of sync operations."""
-
-    IDLE = "idle"
-    SCANNING = "scanning"
-    SYNCING = "syncing"
-    COMPLETED = "completed"
-    FAILED = "failed"
-    WATCHING = "watching"
-
-
-@dataclass
-class ProjectSyncStatus:
-    """Sync status for a single project."""
-
-    project_name: str
-    status: SyncStatus
-    message: str = ""
-    files_total: int = 0
-    files_processed: int = 0
-    error: Optional[str] = None
-
-
-class SyncStatusTracker:
-    """Global tracker for all sync operations."""
-
-    def __init__(self):
-        self._project_statuses: Dict[str, ProjectSyncStatus] = {}
-        self._global_status: SyncStatus = SyncStatus.IDLE
-
-    def start_project_sync(self, project_name: str, files_total: int = 0) -> None:
-        """Start tracking sync for a project."""
-        self._project_statuses[project_name] = ProjectSyncStatus(
-            project_name=project_name,
-            status=SyncStatus.SCANNING,
-            message="Scanning files",
-            files_total=files_total,
-            files_processed=0,
-        )
-        self._update_global_status()
-
-    def update_project_progress(  # pragma: no cover
-        self,
-        project_name: str,
-        status: SyncStatus,
-        message: str = "",
-        files_processed: int = 0,
-        files_total: Optional[int] = None,
-    ) -> None:
-        """Update progress for a project."""
-        if project_name not in self._project_statuses:  # pragma: no cover
-            return
-
-        project_status = self._project_statuses[project_name]
-        project_status.status = status
-        project_status.message = message
-        project_status.files_processed = files_processed
-
-        if files_total is not None:
-            project_status.files_total = files_total
-
-        self._update_global_status()
-
-    def complete_project_sync(self, project_name: str) -> None:
-        """Mark project sync as completed."""
-        if project_name in self._project_statuses:
-            self._project_statuses[project_name].status = SyncStatus.COMPLETED
-            self._project_statuses[project_name].message = "Sync completed"
-            self._update_global_status()
-
-    def fail_project_sync(self, project_name: str, error: str) -> None:
-        """Mark project sync as failed."""
-        if project_name in self._project_statuses:
-            self._project_statuses[project_name].status = SyncStatus.FAILED
-            self._project_statuses[project_name].error = error
-            self._update_global_status()
-
-    def start_project_watch(self, project_name: str) -> None:
-        """Mark project as watching for changes (steady state after sync)."""
-        if project_name in self._project_statuses:
-            self._project_statuses[project_name].status = SyncStatus.WATCHING
-            self._project_statuses[project_name].message = "Watching for changes"
-            self._update_global_status()
-        else:
-            # Create new status if project isn't tracked yet
-            self._project_statuses[project_name] = ProjectSyncStatus(
-                project_name=project_name,
-                status=SyncStatus.WATCHING,
-                message="Watching for changes",
-                files_total=0,
-                files_processed=0,
-            )
-            self._update_global_status()
-
-    def _update_global_status(self) -> None:
-        """Update global status based on project statuses."""
-        if not self._project_statuses:  # pragma: no cover
-            self._global_status = SyncStatus.IDLE
-            return
-
-        statuses = [p.status for p in self._project_statuses.values()]
-
-        if any(s == SyncStatus.FAILED for s in statuses):
-            self._global_status = SyncStatus.FAILED
-        elif any(s in (SyncStatus.SCANNING, SyncStatus.SYNCING) for s in statuses):
-            self._global_status = SyncStatus.SYNCING
-        elif all(s in (SyncStatus.COMPLETED, SyncStatus.WATCHING) for s in statuses):
-            self._global_status = SyncStatus.COMPLETED
-        else:
-            self._global_status = SyncStatus.SYNCING
-
-    @property
-    def global_status(self) -> SyncStatus:
-        """Get overall sync status."""
-        return self._global_status
-
-    @property
-    def is_syncing(self) -> bool:
-        """Check if any sync operation is in progress."""
-        return self._global_status in (SyncStatus.SCANNING, SyncStatus.SYNCING)
-
-    @property
-    def is_ready(self) -> bool:  # pragma: no cover
-        """Check if system is ready (no sync in progress)."""
-        return self._global_status in (SyncStatus.IDLE, SyncStatus.COMPLETED)
-
-    def is_project_ready(self, project_name: str) -> bool:
-        """Check if a specific project is ready for operations.
-
-        Args:
-            project_name: Name of the project to check
-
-        Returns:
-            True if the project is ready (completed, watching, or not tracked),
-            False if the project is syncing, scanning, or failed
-        """
-        project_status = self._project_statuses.get(project_name)
-        if not project_status:
-            # Project not tracked = ready (likely hasn't been synced yet)
-            return True
-
-        return project_status.status in (SyncStatus.COMPLETED, SyncStatus.WATCHING, SyncStatus.IDLE)
-
-    def get_project_status(self, project_name: str) -> Optional[ProjectSyncStatus]:
-        """Get status for a specific project."""
-        return self._project_statuses.get(project_name)
-
-    def get_all_projects(self) -> Dict[str, ProjectSyncStatus]:
-        """Get all project statuses."""
-        return self._project_statuses.copy()
-
-    def get_summary(self) -> str:  # pragma: no cover
-        """Get a user-friendly summary of sync status."""
-        if self._global_status == SyncStatus.IDLE:
-            return "✅ System ready"
-        elif self._global_status == SyncStatus.COMPLETED:
-            return "✅ All projects synced successfully"
-        elif self._global_status == SyncStatus.FAILED:
-            failed_projects = [
-                p.project_name
-                for p in self._project_statuses.values()
-                if p.status == SyncStatus.FAILED
-            ]
-            return f"❌ Sync failed for: {', '.join(failed_projects)}"
-        else:
-            active_projects = [
-                p.project_name
-                for p in self._project_statuses.values()
-                if p.status in (SyncStatus.SCANNING, SyncStatus.SYNCING)
-            ]
-            total_files = sum(p.files_total for p in self._project_statuses.values())
-            processed_files = sum(p.files_processed for p in self._project_statuses.values())
-
-            if total_files > 0:
-                progress_pct = (processed_files / total_files) * 100
-                return f"🔄 Syncing {len(active_projects)} projects ({processed_files}/{total_files} files, {progress_pct:.0f}%)"
-            else:
-                return f"🔄 Syncing {len(active_projects)} projects"
-
-    def clear_completed(self) -> None:
-        """Remove completed project statuses to clean up memory."""
-        self._project_statuses = {
-            name: status
-            for name, status in self._project_statuses.items()
-            if status.status != SyncStatus.COMPLETED
-        }
-        self._update_global_status()
-
-
-# Global sync status tracker instance
-sync_status_tracker = SyncStatusTracker()

src/basic_memory/sync/utils.py

@@ -0,0 +1,23 @@
+"""Utilities for sync operations."""
+
+from typing import Iterator, List, TypeVar
+
+T = TypeVar("T")
+
+
+def chunks(items: List[T], size: int) -> Iterator[List[T]]:
+    """Split a list into chunks of specified size.
+
+    Args:
+        items: List of items to chunk
+        size: Size of each chunk
+
+    Yields:
+        Lists of items, each of specified size (last chunk may be smaller)
+
+    Example:
+        >>> list(chunks([1, 2, 3, 4, 5], 2))
+        [[1, 2], [3, 4], [5]]
+    """
+    for i in range(0, len(items), size):
+        yield items[i : i + size]

src/basic_memory/sync/watch_service.py

@@ -236,6 +236,20 @@ class WatchService:
         # avoid circular imports
         from basic_memory.sync.sync_service import get_sync_service
 
+        # Check if project still exists in configuration before processing
+        # This prevents deleted projects from being recreated by background sync
+        from basic_memory.config import ConfigManager
+
+        config_manager = ConfigManager()
+        if (
+            project.name not in config_manager.projects
+            and project.permalink not in config_manager.projects
+        ):
+            logger.info(
+                f"Skipping sync for deleted project: {project.name}, change_count={len(changes)}"
+            )
+            return
+
         sync_service = await get_sync_service(project)
         file_service = sync_service.file_service
 

src/basic_memory/utils.py

@@ -13,6 +13,49 @@ from loguru import logger
 from unidecode import unidecode
 
 
+def normalize_project_path(path: str) -> str:
+    """Normalize project path by stripping mount point prefix.
+
+    In cloud deployments, the S3 bucket is mounted at /app/data. We strip this
+    prefix from project paths to avoid leaking implementation details and to
+    ensure paths match the actual S3 bucket structure.
+
+    For local paths (including Windows paths), returns the path unchanged.
+
+    Args:
+        path: Project path (e.g., "/app/data/basic-memory-llc" or "C:\\Users\\...")
+
+    Returns:
+        Normalized path (e.g., "/basic-memory-llc" or "C:\\Users\\...")
+
+    Examples:
+        >>> normalize_project_path("/app/data/my-project")
+        '/my-project'
+        >>> normalize_project_path("/my-project")
+        '/my-project'
+        >>> normalize_project_path("app/data/my-project")
+        '/my-project'
+        >>> normalize_project_path("C:\\\\Users\\\\project")
+        'C:\\\\Users\\\\project'
+    """
+    # Check if this is a Windows absolute path (e.g., C:\Users\...)
+    # Windows paths have a drive letter followed by a colon
+    if len(path) >= 2 and path[1] == ":":
+        # Windows absolute path - return unchanged
+        return path
+
+    # Handle both absolute and relative Unix paths
+    normalized = path.lstrip("/")
+    if normalized.startswith("app/data/"):
+        normalized = normalized.removeprefix("app/data/")
+
+    # Ensure leading slash for Unix absolute paths
+    if not normalized.startswith("/"):
+        normalized = "/" + normalized
+
+    return normalized
+
+
 @runtime_checkable
 class PathLike(Protocol):
     """Protocol for objects that can be used as paths."""
@@ -33,10 +76,14 @@ def generate_permalink(file_path: Union[Path, str, PathLike], split_extension: b
 
     Args:
         file_path: Original file path (str, Path, or PathLike)
+        split_extension: Whether to split off and discard file extensions.
+                        When True, uses mimetypes to detect real extensions.
+                        When False, preserves all content including periods.
 
     Returns:
         Normalized permalink that matches validation rules. Converts spaces and underscores
         to hyphens for consistency. Preserves non-ASCII characters like Chinese.
+        Preserves periods in version numbers (e.g., "2.0.0") when they're not real file extensions.
 
     Examples:
         >>> generate_permalink("docs/My Feature.md")
@@ -47,12 +94,26 @@ def generate_permalink(file_path: Union[Path, str, PathLike], split_extension: b
         'design/unified-model-refactor'
         >>> generate_permalink("中文/测试文档.md")
         '中文/测试文档'
+        >>> generate_permalink("Version 2.0.0")
+        'version-2.0.0'
     """
     # Convert Path to string if needed
     path_str = Path(str(file_path)).as_posix()
 
-    # Remove extension (for now, possibly)
-    (base, extension) = os.path.splitext(path_str)
+    # Only split extension if there's a real file extension
+    # Use mimetypes to detect real extensions, avoiding misinterpreting periods in version numbers
+    import mimetypes
+
+    mime_type, _ = mimetypes.guess_type(path_str)
+    has_real_extension = mime_type is not None
+
+    if has_real_extension and split_extension:
+        # Real file extension detected - split it off
+        (base, extension) = os.path.splitext(path_str)
+    else:
+        # No real extension or split_extension=False - process the whole string
+        base = path_str
+        extension = ""
 
     # Check if we have CJK characters that should be preserved
     # CJK ranges: \u4e00-\u9fff (CJK Unified Ideographs), \u3000-\u303f (CJK symbols),
@@ -104,9 +165,9 @@ def generate_permalink(file_path: Union[Path, str, PathLike], split_extension: b
         # Remove apostrophes entirely (don't replace with hyphens)
         text_no_apostrophes = text_with_hyphens.replace("'", "")
 
-        # Replace unsafe chars with hyphens, but preserve CJK characters
+        # Replace unsafe chars with hyphens, but preserve CJK characters and periods
         clean_text = re.sub(
-            r"[^a-z0-9\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf/\-]", "-", text_no_apostrophes
+            r"[^a-z0-9\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf/\-\.]", "-", text_no_apostrophes
         )
     else:
         # Original ASCII-only processing for backward compatibility
@@ -125,8 +186,8 @@ def generate_permalink(file_path: Union[Path, str, PathLike], split_extension: b
         # Remove apostrophes entirely (don't replace with hyphens)
         text_no_apostrophes = text_with_hyphens.replace("'", "")
 
-        # Replace remaining invalid chars with hyphens
-        clean_text = re.sub(r"[^a-z0-9/\-]", "-", text_no_apostrophes)
+        # Replace remaining invalid chars with hyphens, preserving periods
+        clean_text = re.sub(r"[^a-z0-9/\-\.]", "-", text_no_apostrophes)
 
     # Collapse multiple hyphens
     clean_text = re.sub(r"-+", "-", clean_text)
@@ -185,6 +246,21 @@ def setup_logging(
 
     logger.info(f"ENV: '{env}' Log level: '{log_level}' Logging to {log_file}")
 
+    # Bind environment context for structured logging (works in both local and cloud)
+    tenant_id = os.getenv("BASIC_MEMORY_TENANT_ID", "local")
+    fly_app_name = os.getenv("FLY_APP_NAME", "local")
+    fly_machine_id = os.getenv("FLY_MACHINE_ID", "local")
+    fly_region = os.getenv("FLY_REGION", "local")
+
+    logger.configure(
+        extra={
+            "tenant_id": tenant_id,
+            "fly_app_name": fly_app_name,
+            "fly_machine_id": fly_machine_id,
+            "fly_region": fly_region,
+        }
+    )
+
     # Reduce noise from third-party libraries
     noisy_loggers = {
         # HTTP client logs

test-int/cli/test_project_commands_integration.py

@@ -5,13 +5,13 @@ from pathlib import Path
 
 from typer.testing import CliRunner
 
-from basic_memory.cli.main import app
+from basic_memory.cli.main import app as cli_app
 
 
-def test_project_list(app_config, test_project, config_manager):
+def test_project_list(app, app_config, test_project, config_manager):
     """Test 'bm project list' command shows projects."""
     runner = CliRunner()
-    result = runner.invoke(app, ["project", "list"])
+    result = runner.invoke(cli_app, ["project", "list"])
 
     if result.exit_code != 0:
         print(f"STDOUT: {result.stdout}")
@@ -19,13 +19,13 @@ def test_project_list(app_config, test_project, config_manager):
         print(f"Exception: {result.exception}")
     assert result.exit_code == 0
     assert "test-project" in result.stdout
-    assert "✓" in result.stdout  # default marker
+    assert "[X]" in result.stdout  # default marker
 
 
-def test_project_info(app_config, test_project, config_manager):
+def test_project_info(app, app_config, test_project, config_manager):
     """Test 'bm project info' command shows project details."""
     runner = CliRunner()
-    result = runner.invoke(app, ["project", "info", "test-project"])
+    result = runner.invoke(cli_app, ["project", "info", "test-project"])
 
     if result.exit_code != 0:
         print(f"STDOUT: {result.stdout}")
@@ -36,12 +36,12 @@ def test_project_info(app_config, test_project, config_manager):
     assert "Statistics" in result.stdout
 
 
-def test_project_info_json(app_config, test_project, config_manager):
+def test_project_info_json(app, app_config, test_project, config_manager):
     """Test 'bm project info --json' command outputs valid JSON."""
     import json
 
     runner = CliRunner()
-    result = runner.invoke(app, ["project", "info", "test-project", "--json"])
+    result = runner.invoke(cli_app, ["project", "info", "test-project", "--json"])
 
     if result.exit_code != 0:
         print(f"STDOUT: {result.stdout}")
@@ -55,7 +55,7 @@ def test_project_info_json(app_config, test_project, config_manager):
     assert "system" in data
 
 
-def test_project_add_and_remove(app_config, config_manager):
+def test_project_add_and_remove(app, app_config, config_manager):
     """Test adding and removing a project."""
     runner = CliRunner()
 
@@ -65,7 +65,7 @@ def test_project_add_and_remove(app_config, config_manager):
         new_project_path.mkdir()
 
         # Add project
-        result = runner.invoke(app, ["project", "add", "new-project", str(new_project_path)])
+        result = runner.invoke(cli_app, ["project", "add", "new-project", str(new_project_path)])
 
         if result.exit_code != 0:
             print(f"STDOUT: {result.stdout}")
@@ -77,17 +77,17 @@ def test_project_add_and_remove(app_config, config_manager):
         )
 
         # Verify it shows up in list
-        result = runner.invoke(app, ["project", "list"])
+        result = runner.invoke(cli_app, ["project", "list"])
         assert result.exit_code == 0
         assert "new-project" in result.stdout
 
         # Remove project
-        result = runner.invoke(app, ["project", "remove", "new-project"])
+        result = runner.invoke(cli_app, ["project", "remove", "new-project"])
         assert result.exit_code == 0
         assert "removed" in result.stdout.lower() or "deleted" in result.stdout.lower()
 
 
-def test_project_set_default(app_config, config_manager):
+def test_project_set_default(app, app_config, config_manager):
     """Test setting default project."""
     runner = CliRunner()
 
@@ -97,14 +97,16 @@ def test_project_set_default(app_config, config_manager):
         new_project_path.mkdir()
 
         # Add a second project
-        result = runner.invoke(app, ["project", "add", "another-project", str(new_project_path)])
+        result = runner.invoke(
+            cli_app, ["project", "add", "another-project", str(new_project_path)]
+        )
         if result.exit_code != 0:
             print(f"STDOUT: {result.stdout}")
             print(f"STDERR: {result.stderr}")
         assert result.exit_code == 0
 
         # Set as default
-        result = runner.invoke(app, ["project", "default", "another-project"])
+        result = runner.invoke(cli_app, ["project", "default", "another-project"])
         if result.exit_code != 0:
             print(f"STDOUT: {result.stdout}")
             print(f"STDERR: {result.stderr}")
@@ -112,10 +114,52 @@ def test_project_set_default(app_config, config_manager):
         assert "default" in result.stdout.lower()
 
         # Verify in list
-        result = runner.invoke(app, ["project", "list"])
+        result = runner.invoke(cli_app, ["project", "list"])
         assert result.exit_code == 0
-        # The new project should have the checkmark now
+        # The new project should have the [X] marker now
         lines = result.stdout.split("\n")
         for line in lines:
             if "another-project" in line:
-                assert "✓" in line
+                assert "[X]" in line
+
+
+def test_remove_main_project(app, app_config, config_manager):
+    """Test that removing main project then listing projects prevents main from reappearing (issue #397)."""
+    runner = CliRunner()
+
+    # Create separate temp dirs for each project
+    with (
+        tempfile.TemporaryDirectory() as main_dir,
+        tempfile.TemporaryDirectory() as new_default_dir,
+    ):
+        main_path = Path(main_dir)
+        new_default_path = Path(new_default_dir)
+
+        # Ensure main exists
+        result = runner.invoke(cli_app, ["project", "list"])
+        if "main" not in result.stdout:
+            result = runner.invoke(cli_app, ["project", "add", "main", str(main_path)])
+            print(result.stdout)
+            assert result.exit_code == 0
+
+        # Confirm main is present
+        result = runner.invoke(cli_app, ["project", "list"])
+        assert "main" in result.stdout
+
+        # Add a second project
+        result = runner.invoke(cli_app, ["project", "add", "new_default", str(new_default_path)])
+        assert result.exit_code == 0
+
+        # Set new_default as default (if needed)
+        result = runner.invoke(cli_app, ["project", "default", "new_default"])
+        assert result.exit_code == 0
+
+        # Remove main
+        result = runner.invoke(cli_app, ["project", "remove", "main"])
+        assert result.exit_code == 0
+
+        # Confirm only new_default exists and main does not
+        result = runner.invoke(cli_app, ["project", "list"])
+        assert result.exit_code == 0
+        assert "main" not in result.stdout
+        assert "new_default" in result.stdout

test-int/cli/test_sync_commands_integration.py

@@ -1,61 +0,0 @@
-"""Integration tests for sync CLI commands."""
-
-from pathlib import Path
-from typer.testing import CliRunner
-
-from basic_memory.cli.main import app
-
-
-def test_sync_command(app_config, test_project, config_manager, config_home):
-    """Test 'bm sync' command successfully syncs files."""
-    runner = CliRunner()
-
-    # Create a test file
-    test_file = Path(config_home) / "test-note.md"
-    test_file.write_text("# Test Note\n\nThis is a test.")
-
-    # Run sync
-    result = runner.invoke(app, ["sync", "--project", "test-project"])
-
-    if result.exit_code != 0:
-        print(f"STDOUT: {result.stdout}")
-        print(f"STDERR: {result.stderr}")
-    assert result.exit_code == 0
-    assert "sync" in result.stdout.lower() or "initiated" in result.stdout.lower()
-
-
-def test_status_command(app_config, test_project, config_manager, config_home):
-    """Test 'bm status' command shows sync status."""
-    runner = CliRunner()
-
-    # Create a test file
-    test_file = Path(config_home) / "unsynced.md"
-    test_file.write_text("# Unsynced Note\n\nThis file hasn't been synced yet.")
-
-    # Run status
-    result = runner.invoke(app, ["status", "--project", "test-project"])
-
-    if result.exit_code != 0:
-        print(f"STDOUT: {result.stdout}")
-        print(f"STDERR: {result.stderr}")
-    assert result.exit_code == 0
-    # Should show some status output
-    assert len(result.stdout) > 0
-
-
-def test_status_verbose(app_config, test_project, config_manager, config_home):
-    """Test 'bm status --verbose' shows detailed status."""
-    runner = CliRunner()
-
-    # Create a test file
-    test_file = Path(config_home) / "test.md"
-    test_file.write_text("# Test\n\nContent.")
-
-    # Run status with verbose
-    result = runner.invoke(app, ["status", "--project", "test-project", "--verbose"])
-
-    if result.exit_code != 0:
-        print(f"STDOUT: {result.stdout}")
-        print(f"STDERR: {result.stderr}")
-    assert result.exit_code == 0
-    assert len(result.stdout) > 0

test-int/conftest.py

@@ -50,15 +50,16 @@ The `app` fixture ensures FastAPI dependency overrides are active, and
 `mcp_server` provides the MCP server with proper project session initialization.
 """
 
-from typing import AsyncGenerator
+from typing import AsyncGenerator, Literal
 
 import pytest
 import pytest_asyncio
 from pathlib import Path
+from sqlalchemy import text
 
 from httpx import AsyncClient, ASGITransport
 
-from basic_memory.config import BasicMemoryConfig, ProjectConfig, ConfigManager
+from basic_memory.config import BasicMemoryConfig, ProjectConfig, ConfigManager, DatabaseBackend
 from basic_memory.db import engine_session_factory, DatabaseType
 from basic_memory.models import Project
 from basic_memory.repository.project_repository import ProjectRepository
@@ -71,24 +72,89 @@ from basic_memory.deps import get_project_config, get_engine_factory, get_app_co
 from basic_memory.mcp import tools  # noqa: F401
 
 
-@pytest_asyncio.fixture(scope="function")
-async def engine_factory(tmp_path):
-    """Create a SQLite file engine factory for integration testing."""
-    db_path = tmp_path / "test.db"
-    async with engine_session_factory(db_path, DatabaseType.FILESYSTEM) as (
-        engine,
-        session_maker,
-    ):
-        # Initialize database schema
-        from basic_memory.models.base import Base
+@pytest.fixture(
+    params=[
+        pytest.param("sqlite", id="sqlite"),
+        pytest.param("postgres", id="postgres", marks=pytest.mark.postgres),
+    ]
+)
+def db_backend(request) -> Literal["sqlite", "postgres"]:
+    """Parametrize tests to run against both SQLite and Postgres.
 
-        async with engine.begin() as conn:
-            await conn.run_sync(Base.metadata.create_all)
+    Usage:
+        pytest                          # Runs tests against SQLite only (default)
+        pytest -m postgres              # Runs tests against Postgres only
+        pytest -m "not postgres"        # Runs tests against SQLite only
+        pytest --run-all-backends       # Runs tests against both backends
 
-        yield engine, session_maker
+    Note: Only tests that use database fixtures (engine_factory, session_maker, etc.)
+    will be parametrized. Tests that don't use the database won't be affected.
+    """
+    return request.param
 
 
-@pytest_asyncio.fixture(scope="function")
+@pytest_asyncio.fixture
+async def engine_factory(
+    app_config,
+    config_manager,
+    db_backend: Literal["sqlite", "postgres"],
+    tmp_path,
+) -> AsyncGenerator[tuple, None]:
+    """Create engine and session factory for the configured database backend."""
+    from basic_memory.models.search import CREATE_SEARCH_INDEX
+    from basic_memory import db
+
+    # Determine database type based on backend
+    if db_backend == "postgres":
+        db_type = DatabaseType.FILESYSTEM
+    else:
+        db_type = DatabaseType.FILESYSTEM  # Integration tests use file-based SQLite
+
+    # Use tmp_path for SQLite, use config database_path for Postgres
+    if db_backend == "sqlite":
+        db_path = tmp_path / "test.db"
+    else:
+        db_path = app_config.database_path
+
+    if db_backend == "postgres":
+        # Postgres: Create fresh engine for each test with full schema reset
+        config_manager._config = app_config
+
+        # Use context manager to handle engine disposal properly
+        async with engine_session_factory(db_path, db_type) as (engine, session_maker):
+            # Drop and recreate schema for complete isolation
+            async with engine.begin() as conn:
+                await conn.execute(text("DROP SCHEMA IF EXISTS public CASCADE"))
+                await conn.execute(text("CREATE SCHEMA public"))
+                await conn.execute(text("GRANT ALL ON SCHEMA public TO basic_memory_user"))
+                await conn.execute(text("GRANT ALL ON SCHEMA public TO public"))
+
+            # Run migrations to create production tables
+            from basic_memory.db import run_migrations
+
+            await run_migrations(app_config, db_type)
+
+            yield engine, session_maker
+
+    else:
+        # SQLite: Create fresh database (fast with tmp files)
+        async with engine_session_factory(db_path, db_type) as (engine, session_maker):
+            # Create all tables via ORM
+            from basic_memory.models.base import Base
+
+            async with engine.begin() as conn:
+                await conn.run_sync(Base.metadata.create_all)
+
+            # Drop any SearchIndex ORM table, then create FTS5 virtual table
+            async with db.scoped_session(session_maker) as session:
+                await session.execute(text("DROP TABLE IF EXISTS search_index"))
+                await session.execute(CREATE_SEARCH_INDEX)
+                await session.commit()
+
+            yield engine, session_maker
+
+
+@pytest_asyncio.fixture
 async def test_project(config_home, engine_factory) -> Project:
     """Create a test project."""
     project_data = {
@@ -113,14 +179,27 @@ def config_home(tmp_path, monkeypatch) -> Path:
     return tmp_path
 
 
-@pytest.fixture(scope="function", autouse=True)
-def app_config(config_home, tmp_path, monkeypatch) -> BasicMemoryConfig:
+@pytest.fixture
+def app_config(
+    config_home, db_backend: Literal["sqlite", "postgres"], tmp_path, monkeypatch
+) -> BasicMemoryConfig:
     """Create test app configuration."""
     # Disable cloud mode for CLI tests
     monkeypatch.setenv("BASIC_MEMORY_CLOUD_MODE", "false")
 
     # Create a basic config with test-project like unit tests do
     projects = {"test-project": str(config_home)}
+
+    # Configure database backend based on test parameter
+    if db_backend == "postgres":
+        database_backend = DatabaseBackend.POSTGRES
+        database_url = (
+            "postgresql+asyncpg://basic_memory_user:dev_password@localhost:5433/basic_memory_test"
+        )
+    else:
+        database_backend = DatabaseBackend.SQLITE
+        database_url = None
+
     app_config = BasicMemoryConfig(
         env="test",
         projects=projects,
@@ -128,12 +207,19 @@ def app_config(config_home, tmp_path, monkeypatch) -> BasicMemoryConfig:
         default_project_mode=False,  # Match real-world usage - tools must pass explicit project
         update_permalinks_on_move=True,
         cloud_mode=False,  # Explicitly disable cloud mode
+        database_backend=database_backend,
+        database_url=database_url,
     )
     return app_config
 
 
-@pytest.fixture(scope="function", autouse=True)
+@pytest.fixture
 def config_manager(app_config: BasicMemoryConfig, config_home) -> ConfigManager:
+    # Invalidate config cache to ensure clean state for each test
+    from basic_memory import config as config_module
+
+    config_module._CONFIG_CACHE = None
+
     config_manager = ConfigManager()
     # Update its paths to use the test directory
     config_manager.config_dir = config_home / ".basic-memory"
@@ -145,7 +231,7 @@ def config_manager(app_config: BasicMemoryConfig, config_home) -> ConfigManager:
     return config_manager
 
 
-@pytest.fixture(scope="function", autouse=True)
+@pytest.fixture
 def project_config(test_project):
     """Create test project configuration."""
 
@@ -157,7 +243,7 @@ def project_config(test_project):
     return project_config
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture
 def app(app_config, project_config, engine_factory, test_project, config_manager) -> FastAPI:
     """Create test FastAPI application with single project."""
 
@@ -172,20 +258,25 @@ def app(app_config, project_config, engine_factory, test_project, config_manager
     return app
 
 
-@pytest_asyncio.fixture(scope="function")
-async def search_service(engine_factory, test_project):
-    """Create and initialize search service for integration tests."""
-    from basic_memory.repository.search_repository import SearchRepository
+@pytest_asyncio.fixture
+async def search_service(engine_factory, test_project, app_config):
+    """Create and initialize search service for integration tests.
+
+    Uses app_config fixture to determine database backend - no patching needed.
+    """
     from basic_memory.repository.entity_repository import EntityRepository
     from basic_memory.services.file_service import FileService
     from basic_memory.services.search_service import SearchService
     from basic_memory.markdown.markdown_processor import MarkdownProcessor
     from basic_memory.markdown import EntityParser
 
+    from basic_memory.repository.search_repository import create_search_repository
+
     engine, session_maker = engine_factory
 
-    # Create repositories
-    search_repository = SearchRepository(session_maker, project_id=test_project.id)
+    # Use factory function to create appropriate search repository
+    search_repository = create_search_repository(session_maker, project_id=test_project.id)
+
     entity_repository = EntityRepository(session_maker, project_id=test_project.id)
 
     # Create file service
@@ -199,7 +290,7 @@ async def search_service(engine_factory, test_project):
     return service
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture
 def mcp_server(config_manager, search_service):
     # Import mcp instance
     from basic_memory.mcp.server import mcp as server
@@ -213,7 +304,7 @@ def mcp_server(config_manager, search_service):
     return server
 
 
-@pytest_asyncio.fixture(scope="function")
+@pytest_asyncio.fixture
 async def client(app: FastAPI) -> AsyncGenerator[AsyncClient, None]:
     """Create test client that both MCP and tests will use."""
     async with AsyncClient(transport=ASGITransport(app=app), base_url="http://test") as client:

test-int/mcp/test_write_note_integration.py

@@ -9,9 +9,10 @@ from textwrap import dedent
 
 import pytest
 from fastmcp import Client
-from unittest.mock import patch
 
 from basic_memory.config import ConfigManager
+from basic_memory.schemas.project_info import ProjectItem
+from pathlib import Path
 
 
 @pytest.mark.asyncio
@@ -313,79 +314,68 @@ async def test_write_note_preserve_frontmatter(mcp_server, app, test_project):
 
 
 @pytest.mark.asyncio
-async def test_write_note_kebab_filenames_basic(mcp_server, test_project):
+async def test_write_note_kebab_filenames_basic(mcp_server, app, test_project, app_config):
     """Test note creation with kebab_filenames=True and invalid filename characters."""
 
-    config = ConfigManager().config
-    curr_config_val = config.kebab_filenames
-    config.kebab_filenames = True
+    app_config.kebab_filenames = True
+    ConfigManager().save_config(app_config)
 
-    with patch.object(ConfigManager, "config", config):
-        async with Client(mcp_server) as client:
-            result = await client.call_tool(
-                "write_note",
-                {
-                    "project": test_project.name,
-                    "title": "My Note: With/Invalid|Chars?",
-                    "folder": "my-folder",
-                    "content": "Testing kebab-case and invalid characters.",
-                    "tags": "kebab,invalid,filename",
-                },
-            )
+    async with Client(mcp_server) as client:
+        result = await client.call_tool(
+            "write_note",
+            {
+                "project": test_project.name,
+                "title": "My Note: With/Invalid|Chars?",
+                "folder": "my-folder",
+                "content": "Testing kebab-case and invalid characters.",
+                "tags": "kebab,invalid,filename",
+            },
+        )
 
-            assert len(result.content) == 1
-            response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
+        assert len(result.content) == 1
+        response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
 
-            # File path and permalink should be kebab-case and sanitized
-            assert f"project: {test_project.name}" in response_text
-            assert "file_path: my-folder/my-note-with-invalid-chars.md" in response_text
-            assert "permalink: my-folder/my-note-with-invalid-chars" in response_text
-            assert f"[Session: Using project '{test_project.name}']" in response_text
-
-    # Restore original config value
-    config.kebab_filenames = curr_config_val
+        # File path and permalink should be kebab-case and sanitized
+        assert f"project: {test_project.name}" in response_text
+        assert "file_path: my-folder/my-note-with-invalid-chars.md" in response_text
+        assert "permalink: my-folder/my-note-with-invalid-chars" in response_text
+        assert f"[Session: Using project '{test_project.name}']" in response_text
 
 
 @pytest.mark.asyncio
-async def test_write_note_kebab_filenames_repeat_invalid(mcp_server, test_project):
+async def test_write_note_kebab_filenames_repeat_invalid(mcp_server, app, test_project, app_config):
     """Test note creation with multiple invalid and repeated characters."""
 
-    config = ConfigManager().config
-    curr_config_val = config.kebab_filenames
-    config.kebab_filenames = True
+    app_config.kebab_filenames = True
+    ConfigManager().save_config(app_config)
 
-    with patch.object(ConfigManager, "config", config):
-        async with Client(mcp_server) as client:
-            result = await client.call_tool(
-                "write_note",
-                {
-                    "project": test_project.name,
-                    "title": 'Crazy<>:"|?*Note/Name',
-                    "folder": "my-folder",
-                    "content": "Should be fully kebab-case and safe.",
-                    "tags": "crazy,filename,test",
-                },
-            )
+    async with Client(mcp_server) as client:
+        result = await client.call_tool(
+            "write_note",
+            {
+                "project": test_project.name,
+                "title": 'Crazy<>:"|?*Note/Name',
+                "folder": "my-folder",
+                "content": "Should be fully kebab-case and safe.",
+                "tags": "crazy,filename,test",
+            },
+        )
 
-            assert len(result.content) == 1
-            response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
+        assert len(result.content) == 1
+        response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
 
-            assert f"project: {test_project.name}" in response_text
-            assert "file_path: my-folder/crazy-note-name.md" in response_text
-            assert "permalink: my-folder/crazy-note-name" in response_text
-            assert f"[Session: Using project '{test_project.name}']" in response_text
-
-    # Restore original config value
-    config.kebab_filenames = curr_config_val
+        assert f"project: {test_project.name}" in response_text
+        assert "file_path: my-folder/crazy-note-name.md" in response_text
+        assert "permalink: my-folder/crazy-note-name" in response_text
+        assert f"[Session: Using project '{test_project.name}']" in response_text
 
 
 @pytest.mark.asyncio
-async def test_write_note_file_path_os_path_join(mcp_server, test_project):
+async def test_write_note_file_path_os_path_join(mcp_server, app, test_project, app_config):
     """Test that os.path.join logic in Entity.file_path works for various folder/title combinations."""
 
-    config = ConfigManager().config
-    curr_config_val = config.kebab_filenames
-    config.kebab_filenames = True
+    app_config.kebab_filenames = True
+    ConfigManager().save_config(app_config)
 
     test_cases = [
         # (folder, title, expected file_path, expected permalink)
@@ -407,35 +397,31 @@ async def test_write_note_file_path_os_path_join(mcp_server, test_project):
         ("folder//subfolder", "Note", "folder/subfolder/note.md", "folder/subfolder/note"),
     ]
 
-    with patch.object(ConfigManager, "config", config):
-        async with Client(mcp_server) as client:
-            for folder, title, expected_path, expected_permalink in test_cases:
-                result = await client.call_tool(
-                    "write_note",
-                    {
-                        "project": test_project.name,
-                        "title": title,
-                        "folder": folder,
-                        "content": "Testing os.path.join logic.",
-                        "tags": "integration,ospath",
-                    },
-                )
+    async with Client(mcp_server) as client:
+        for folder, title, expected_path, expected_permalink in test_cases:
+            result = await client.call_tool(
+                "write_note",
+                {
+                    "project": test_project.name,
+                    "title": title,
+                    "folder": folder,
+                    "content": "Testing os.path.join logic.",
+                    "tags": "integration,ospath",
+                },
+            )
 
-                assert len(result.content) == 1
-                response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
-                print(response_text)
+            assert len(result.content) == 1
+            response_text = result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
+            print(response_text)
 
-                assert f"project: {test_project.name}" in response_text
-                assert f"file_path: {expected_path}" in response_text
-                assert f"permalink: {expected_permalink}" in response_text
-                assert f"[Session: Using project '{test_project.name}']" in response_text
-
-    # Restore original config value
-    config.kebab_filenames = curr_config_val
+            assert f"project: {test_project.name}" in response_text
+            assert f"file_path: {expected_path}" in response_text
+            assert f"permalink: {expected_permalink}" in response_text
+            assert f"[Session: Using project '{test_project.name}']" in response_text
 
 
 @pytest.mark.asyncio
-async def test_write_note_project_path_validation(mcp_server, test_project):
+async def test_write_note_project_path_validation(mcp_server, app, test_project):
     """Test that ProjectItem.home uses expanded path, not name (Issue #340).
 
     Regression test verifying that:
@@ -446,8 +432,6 @@ async def test_write_note_project_path_validation(mcp_server, test_project):
     the project name and path happen to be the same. The fix in src/basic_memory/schemas/project_info.py:186
     ensures .expanduser() is called, which is critical for paths with ~ like "~/Documents/Test BiSync".
     """
-    from basic_memory.schemas.project_info import ProjectItem
-    from pathlib import Path
 
     # Test the fix directly: ProjectItem.home should expand tilde paths
     project_with_tilde = ProjectItem(

test-int/test_db_wal_mode.py

@@ -10,8 +10,11 @@ from sqlalchemy import text
 
 
 @pytest.mark.asyncio
-async def test_wal_mode_enabled(engine_factory):
+async def test_wal_mode_enabled(engine_factory, db_backend):
     """Test that WAL mode is enabled on filesystem database connections."""
+    if db_backend == "postgres":
+        pytest.skip("SQLite-specific test - PRAGMA commands not supported in Postgres")
+
     engine, _ = engine_factory
 
     # Execute a query to verify WAL mode is enabled
@@ -24,8 +27,11 @@ async def test_wal_mode_enabled(engine_factory):
 
 
 @pytest.mark.asyncio
-async def test_busy_timeout_configured(engine_factory):
+async def test_busy_timeout_configured(engine_factory, db_backend):
     """Test that busy timeout is configured for database connections."""
+    if db_backend == "postgres":
+        pytest.skip("SQLite-specific test - PRAGMA commands not supported in Postgres")
+
     engine, _ = engine_factory
 
     async with engine.connect() as conn:
@@ -37,8 +43,11 @@ async def test_busy_timeout_configured(engine_factory):
 
 
 @pytest.mark.asyncio
-async def test_synchronous_mode_configured(engine_factory):
+async def test_synchronous_mode_configured(engine_factory, db_backend):
     """Test that synchronous mode is set to NORMAL for performance."""
+    if db_backend == "postgres":
+        pytest.skip("SQLite-specific test - PRAGMA commands not supported in Postgres")
+
     engine, _ = engine_factory
 
     async with engine.connect() as conn:
@@ -50,8 +59,11 @@ async def test_synchronous_mode_configured(engine_factory):
 
 
 @pytest.mark.asyncio
-async def test_cache_size_configured(engine_factory):
+async def test_cache_size_configured(engine_factory, db_backend):
     """Test that cache size is configured for performance."""
+    if db_backend == "postgres":
+        pytest.skip("SQLite-specific test - PRAGMA commands not supported in Postgres")
+
     engine, _ = engine_factory
 
     async with engine.connect() as conn:
@@ -63,8 +75,11 @@ async def test_cache_size_configured(engine_factory):
 
 
 @pytest.mark.asyncio
-async def test_temp_store_configured(engine_factory):
+async def test_temp_store_configured(engine_factory, db_backend):
     """Test that temp_store is set to MEMORY."""
+    if db_backend == "postgres":
+        pytest.skip("SQLite-specific test - PRAGMA commands not supported in Postgres")
+
     engine, _ = engine_factory
 
     async with engine.connect() as conn:
@@ -76,42 +91,61 @@ async def test_temp_store_configured(engine_factory):
 
 
 @pytest.mark.asyncio
-async def test_windows_locking_mode_when_on_windows(tmp_path):
+@pytest.mark.windows
+@pytest.mark.skipif(
+    __import__("os").name != "nt", reason="Windows-specific test - only runs on Windows platform"
+)
+async def test_windows_locking_mode_when_on_windows(tmp_path, monkeypatch, config_manager):
     """Test that Windows-specific locking mode is set when running on Windows."""
     from basic_memory.db import engine_session_factory, DatabaseType
+    from basic_memory.config import DatabaseBackend
+
+    # Force SQLite backend for this SQLite-specific test
+    config_manager.config.database_backend = DatabaseBackend.SQLITE
+
+    # Set HOME environment variable
+    monkeypatch.setenv("HOME", str(tmp_path))
+    monkeypatch.setenv("BASIC_MEMORY_HOME", str(tmp_path / "basic-memory"))
 
     db_path = tmp_path / "test_windows.db"
 
-    with patch("os.name", "nt"):
-        # Need to patch at module level where it's imported
-        with patch("basic_memory.db.os.name", "nt"):
-            async with engine_session_factory(db_path, DatabaseType.FILESYSTEM) as (
-                engine,
-                _,
-            ):
-                async with engine.connect() as conn:
-                    result = await conn.execute(text("PRAGMA locking_mode"))
-                    locking_mode = result.fetchone()[0]
+    async with engine_session_factory(db_path, DatabaseType.FILESYSTEM) as (
+        engine,
+        _,
+    ):
+        async with engine.connect() as conn:
+            result = await conn.execute(text("PRAGMA locking_mode"))
+            locking_mode = result.fetchone()[0]
 
-                    # Locking mode should be NORMAL on Windows
-                    assert locking_mode.upper() == "NORMAL"
+            # Locking mode should be NORMAL on Windows
+            assert locking_mode.upper() == "NORMAL"
 
 
 @pytest.mark.asyncio
-async def test_null_pool_on_windows(tmp_path):
+@pytest.mark.windows
+@pytest.mark.skipif(
+    __import__("os").name != "nt", reason="Windows-specific test - only runs on Windows platform"
+)
+async def test_null_pool_on_windows(tmp_path, monkeypatch):
     """Test that NullPool is used on Windows to avoid connection pooling issues."""
     from basic_memory.db import engine_session_factory, DatabaseType
     from sqlalchemy.pool import NullPool
 
+    # Set HOME environment variable
+    monkeypatch.setenv("HOME", str(tmp_path))
+    monkeypatch.setenv("BASIC_MEMORY_HOME", str(tmp_path / "basic-memory"))
+
     db_path = tmp_path / "test_windows_pool.db"
 
-    with patch("basic_memory.db.os.name", "nt"):
-        async with engine_session_factory(db_path, DatabaseType.FILESYSTEM) as (engine, _):
-            # Engine should be using NullPool on Windows
-            assert isinstance(engine.pool, NullPool)
+    async with engine_session_factory(db_path, DatabaseType.FILESYSTEM) as (engine, _):
+        # Engine should be using NullPool on Windows
+        assert isinstance(engine.pool, NullPool)
 
 
 @pytest.mark.asyncio
+@pytest.mark.skipif(
+    __import__("os").name == "nt", reason="Non-Windows test - cannot mock POSIX paths on Windows"
+)
 async def test_regular_pool_on_non_windows(tmp_path):
     """Test that regular pooling is used on non-Windows platforms."""
     from basic_memory.db import engine_session_factory, DatabaseType
@@ -126,7 +160,11 @@ async def test_regular_pool_on_non_windows(tmp_path):
 
 
 @pytest.mark.asyncio
-async def test_memory_database_no_null_pool_on_windows(tmp_path):
+@pytest.mark.windows
+@pytest.mark.skipif(
+    __import__("os").name != "nt", reason="Windows-specific test - only runs on Windows platform"
+)
+async def test_memory_database_no_null_pool_on_windows(tmp_path, monkeypatch):
     """Test that in-memory databases do NOT use NullPool even on Windows.
 
     NullPool closes connections immediately, which destroys in-memory databases.
@@ -135,9 +173,12 @@ async def test_memory_database_no_null_pool_on_windows(tmp_path):
     from basic_memory.db import engine_session_factory, DatabaseType
     from sqlalchemy.pool import NullPool
 
+    # Set HOME environment variable
+    monkeypatch.setenv("HOME", str(tmp_path))
+    monkeypatch.setenv("BASIC_MEMORY_HOME", str(tmp_path / "basic-memory"))
+
     db_path = tmp_path / "test_memory.db"
 
-    with patch("basic_memory.db.os.name", "nt"):
-        async with engine_session_factory(db_path, DatabaseType.MEMORY) as (engine, _):
-            # In-memory databases should NOT use NullPool on Windows
-            assert not isinstance(engine.pool, NullPool)
+    async with engine_session_factory(db_path, DatabaseType.MEMORY) as (engine, _):
+        # In-memory databases should NOT use NullPool on Windows
+        assert not isinstance(engine.pool, NullPool)