chore: update version to 0.14.4 for v0.14.4 release

- Replace bare except clauses with Exception in legal_file_inventory.py
- Remove unused variables in test files
- Prepare codebase for v0.14.4 release

.github/workflows/test.yml

@@ -14,11 +14,12 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, windows-latest]
         python-version: [ "3.12" ]
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
@@ -35,10 +36,18 @@ jobs:
         run: |
           pip install uv
 
-      - name: Install just
+      - name: Install just (Linux/macOS)
+        if: runner.os != 'Windows'
         run: |
           curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to /usr/local/bin
 
+      - name: Install just (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          # Install just using Chocolatey (pre-installed on GitHub Actions Windows runners)
+          choco install just --yes
+        shell: pwsh
+
       - name: Create virtual env
         run: |
           uv venv
@@ -54,4 +63,4 @@ jobs:
       - name: Run tests
         run: |
           uv pip install pytest pytest-cov
-          just test
+          just test

CLA.md

@@ -1,34 +1,71 @@
-Developer Certificate of Origin
-Version 1.1
-https://developercertificate.org/
+# Contributor License Agreement
 
-Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
+## Copyright Assignment and License Grant
 
-Everyone is permitted to copy and distribute verbatim copies of this
-license document, but changing it is not allowed.
+By signing this Contributor License Agreement ("Agreement"), you accept and agree to the following terms and conditions
+for your present and future Contributions submitted
+to Basic Machines LLC. Except for the license granted herein to Basic Machines LLC and recipients of software
+distributed by Basic Machines LLC, you reserve all right,
+title, and interest in and to your Contributions.
 
-Developer's Certificate of Origin 1.1
+### 1. Definitions
 
-By making a contribution to this project, I certify that:
+"You" (or "Your") shall mean the copyright owner or legal entity authorized by the copyright owner that is making this
+Agreement with Basic Machines LLC.
 
-(a) The contribution was created in whole or in part by me and I
-have the right to submit it under the open source license
-indicated in the file; or
+"Contribution" shall mean any original work of authorship, including any modifications or additions to an existing work,
+that is intentionally submitted by You to Basic
+Machines LLC for inclusion in, or documentation of, any of the products owned or managed by Basic Machines LLC (the "
+Work").
 
-(b) The contribution is based upon previous work that, to the best
-of my knowledge, is covered under an appropriate open source
-license and I have the right under that license to submit that
-work with modifications, whether created in whole or in part
-by me, under the same open source license (unless I am
-permitted to submit under a different license), as indicated
-in the file; or
+### 2. Grant of Copyright License
 
-(c) The contribution was provided directly to me by some other
-person who certified (a), (b) or (c) and I have not modified
-it.
+Subject to the terms and conditions of this Agreement, You hereby grant to Basic Machines LLC and to recipients of
+software distributed by Basic Machines LLC a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the
+Work, and to permit persons to whom the Work is furnished to do so.
 
-(d) I understand and agree that this project and the contribution
-are public and that a record of the contribution (including all
-personal information I submit with it, including my sign-off) is
-maintained indefinitely and may be redistributed consistent with
-this project or the open source license(s) involved.
+### 3. Assignment of Copyright
+
+You hereby assign to Basic Machines LLC all right, title, and interest worldwide in all Copyright covering your
+Contributions. Basic Machines LLC may license the
+Contributions under any license terms, including copyleft, permissive, commercial, or proprietary licenses.
+
+### 4. Grant of Patent License
+
+Subject to the terms and conditions of this Agreement, You hereby grant to Basic Machines LLC and to recipients of
+software distributed by Basic Machines LLC a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to
+make, have made, use, offer to sell, sell, import, and
+otherwise transfer the Work.
+
+### 5. Developer Certificate of Origin
+
+By making a Contribution to this project, You certify that:
+
+(a) The Contribution was created in whole or in part by You and You have the right to submit it under this Agreement; or
+
+(b) The Contribution is based upon previous work that, to the best of Your knowledge, is covered under an appropriate
+open source license and You have the right under that
+license to submit that work with modifications, whether created in whole or in part by You, under this Agreement; or
+
+(c) The Contribution was provided directly to You by some other person who certified (a), (b) or (c) and You have not
+modified it.
+
+(d) You understand and agree that this project and the Contribution are public and that a record of the Contribution (
+including all personal information You submit with
+it, including Your sign-off) is maintained indefinitely and may be redistributed consistent with this project or the
+open source license(s) involved.
+
+### 6. Representations
+
+You represent that you are legally entitled to grant the above license and assignment. If your employer(s) has rights to
+intellectual property that you create that
+includes your Contributions, you represent that you have received permission to make Contributions on behalf of that
+employer, or that your employer has waived such rights
+for your Contributions to Basic Machines LLC.
+
+---
+
+This Agreement is effective as of the date you first submit a Contribution to Basic Machines LLC.

CLAUDE.md

@@ -14,15 +14,15 @@ See the [README.md](README.md) file for a project overview.
 
 ### Build and Test Commands
 
-- Install: `just install` or `pip install -e ".[dev]"`
-- Run tests: `uv run pytest -p pytest_mock -v` or `just test`
+- Install: `make install` or `pip install -e ".[dev]"`
+- Run tests: `uv run pytest -p pytest_mock -v` or `make test`
 - Single test: `pytest tests/path/to/test_file.py::test_function_name`
-- Lint: `just lint` or `ruff check . --fix`
-- Type check: `just type-check` or `uv run pyright`
-- Format: `just format` or `uv run ruff format .`
-- Run all code checks: `just check` (runs lint, format, type-check, test)
-- Create db migration: `just migration "Your migration message"`
-- Run development MCP Inspector: `just run-inspector`
+- Lint: `make lint` or `ruff check . --fix`
+- Type check: `make type-check` or `uv run pyright`
+- Format: `make format` or `uv run ruff format .`
+- Run all code checks: `make check` (runs lint, format, type-check, test)
+- Create db migration: `make migration m="Your migration message"`
+- Run development MCP Inspector: `make run-inspector`
 
 ### Code Style Guidelines
 
@@ -37,7 +37,6 @@ See the [README.md](README.md) file for a project overview.
 - API uses FastAPI for endpoints
 - Follow the repository pattern for data access
 - Tools communicate to api routers via the httpx ASGI client (in process)
-- avoid using "private" functions in modules or classes (prepended with _)
 
 ### Codebase Architecture
 
@@ -65,7 +64,6 @@ See the [README.md](README.md) file for a project overview.
 - Test database uses in-memory SQLite
 - Avoid creating mocks in tests in most circumstances.
 - Each test runs in a standalone environment with in memory SQLite and tmp_file directory
-- Do not use mocks in tests if possible. Tests run with an in memory sqlite db, so they are not needed. See fixtures in conftest.py
 
 ## BASIC MEMORY PRODUCT USAGE
 
@@ -97,29 +95,18 @@ See the [README.md](README.md) file for a project overview.
 
   **Content Management:**
     - `write_note(title, content, folder, tags)` - Create/update markdown notes with semantic observations and relations
-    - `read_note(identifier, page, page_size)` - Read notes by title, permalink, or memory:// URL with knowledge graph awareness
-    - `edit_note(identifier, operation, content)` - Edit notes incrementally (append, prepend, find/replace, section replace)
-    - `move_note(identifier, destination_path)` - Move notes with database consistency and search reindexing
-    - `view_note(identifier)` - Display notes as formatted artifacts for better readability in Claude Desktop
-    - `read_content(path)` - Read raw file content (text, images, binaries) without knowledge graph processing
-    - `delete_note(identifier)` - Delete notes from knowledge base
-
-  **Project Management:**
-    - `list_memory_projects()` - List all available projects with status indicators
-    - `switch_project(project_name)` - Switch to different project context during conversations
-    - `get_current_project()` - Show currently active project with statistics
-    - `create_memory_project(name, path, set_default)` - Create new Basic Memory projects
-    - `delete_project(name)` - Delete projects from configuration and database
-    - `set_default_project(name)` - Set default project in config
-    - `sync_status()` - Check file synchronization status and background operations
+    - `read_note(identifier, page, page_size)` - Read notes by title, permalink, or memory:// URL with knowledge graph
+      awareness
+    - `read_file(path)` - Read raw file content (text, images, binaries) without knowledge graph processing
 
   **Knowledge Graph Navigation:**
-    - `build_context(url, depth, timeframe)` - Navigate the knowledge graph via memory:// URLs for conversation continuity
-    - `recent_activity(type, depth, timeframe)` - Get recently updated information with specified timeframe (e.g., "1d", "1 week")
-    - `list_directory(dir_name, depth, file_name_glob)` - List directory contents with filtering and depth control
+    - `build_context(url, depth, timeframe)` - Navigate the knowledge graph via memory:// URLs for conversation
+      continuity
+    - `recent_activity(type, depth, timeframe)` - Get recently updated information with specified timeframe (e.g., "
+      1d", "1 week")
 
   **Search & Discovery:**
-    - `search_notes(query, page, page_size)` - Full-text search across all content with filtering options
+    - `search(query, page, page_size)` - Full-text search across all content with filtering options
 
   **Visualization:**
     - `canvas(nodes, edges, title, folder)` - Generate Obsidian canvas files for knowledge graph visualization
@@ -127,7 +114,7 @@ See the [README.md](README.md) file for a project overview.
 - MCP Prompts for better AI interaction:
     - `ai_assistant_guide()` - Guidance on effectively using Basic Memory tools for AI assistants
     - `continue_conversation(topic, timeframe)` - Continue previous conversations with relevant historical context
-    - `search_notes(query, after_date)` - Search with detailed, formatted results for better context understanding
+    - `search(query, after_date)` - Search with detailed, formatted results for better context understanding
     - `recent_activity(timeframe)` - View recently changed items with formatted output
     - `json_canvas_spec()` - Full JSON Canvas specification for Obsidian visualization
 
@@ -147,32 +134,30 @@ could achieve independently.
 
 ## GitHub Integration
 
-Basic Memory uses Claude directly into the development workflow through GitHub:
+Basic Memory has taken AI-Human collaboration to the next level by integrating Claude directly into the development workflow through GitHub:
 
 ### GitHub MCP Tools
 
-Using the GitHub Model Context Protocol server, Claude can:
+Using the GitHub Model Context Protocol server, Claude can now:
 
 - **Repository Management**:
-    - View repository files and structure
-    - Read file contents
-    - Create new branches
-    - Create and update files
+  - View repository files and structure
+  - Read file contents
+  - Create new branches
+  - Create and update files
 
 - **Issue Management**:
-    - Create new issues
-    - Comment on existing issues
-    - Close and update issues
-    - Search across issues
+  - Create new issues
+  - Comment on existing issues
+  - Close and update issues
+  - Search across issues
 
 - **Pull Request Workflow**:
-    - Create pull requests
-    - Review code changes
-    - Add comments to PRs
+  - Create pull requests
+  - Review code changes
+  - Add comments to PRs
 
-This integration enables Claude to participate as a full team member in the development process, not just as a code
-generation tool. Claude's GitHub account ([bm-claudeai](https://github.com/bm-claudeai)) is a member of the Basic
-Machines organization with direct contributor access to the codebase.
+This integration enables Claude to participate as a full team member in the development process, not just as a code generation tool. Claude's GitHub account ([bm-claudeai](https://github.com/bm-claudeai)) is a member of the Basic Machines organization with direct contributor access to the codebase.
 
 ### Collaborative Development Process
 
@@ -183,75 +168,4 @@ With GitHub integration, the development workflow includes:
 3. **Branch management** - Claude can create feature branches for implementations
 4. **Documentation maintenance** - Claude can keep documentation updated as the code evolves
 
-With this integration, the AI assistant is a full-fledged team member rather than just a tool for generating code
-snippets.
-
-
-### Basic Memory Pro
-
-Basic Memory Pro is a desktop GUI application that wraps the basic-memory CLI/MCP tools:
-
-- Built with Tauri (Rust), React (TypeScript), and a Python FastAPI sidecar
-- Provides visual knowledge graph exploration and project management
-- Uses the same core codebase but adds a desktop-friendly interface
-- Project configuration is shared between CLI and Pro versions
-- Multiple project support with visual switching interface
-
-local repo: /Users/phernandez/dev/basicmachines/basic-memory-pro
-github: https://github.com/basicmachines-co/basic-memory-pro
-
-## Release and Version Management
-
-Basic Memory uses `uv-dynamic-versioning` for automatic version management based on git tags:
-
-### Version Types
-- **Development versions**: Automatically generated from commits (e.g., `0.12.4.dev26+468a22f`)
-- **Beta releases**: Created by tagging with beta suffixes (e.g., `v0.13.0b1`, `v0.13.0rc1`)
-- **Stable releases**: Created by tagging with version numbers (e.g., `v0.13.0`)
-
-### Release Workflows
-
-#### Development Builds (Automatic)
-- Triggered on every push to `main` branch
-- Publishes dev versions like `0.12.4.dev26+468a22f` to PyPI
-- Allows continuous testing of latest changes
-- Users install with: `pip install basic-memory --pre --force-reinstall`
-
-#### Beta/RC Releases (Manual)
-- Create beta tag: `git tag v0.13.0b1 && git push origin v0.13.0b1`
-- Automatically builds and publishes to PyPI as pre-release
-- Users install with: `pip install basic-memory --pre`
-- Use for milestone testing before stable release
-
-#### Stable Releases (Automated)
-- Use the automated release system: `just release v0.13.0`
-- Includes comprehensive quality checks (lint, format, type-check, tests)
-- Automatically updates version in `__init__.py`
-- Creates git tag and pushes to GitHub
-- Triggers GitHub Actions workflow for:
-  - PyPI publication
-  - Homebrew formula update (requires HOMEBREW_TOKEN secret)
-
-**Manual method (legacy):**
-- Create version tag: `git tag v0.13.0 && git push origin v0.13.0`
-
-#### Homebrew Formula Updates
-- Automatically triggered after successful PyPI release for **stable releases only**
-- **Stable releases** (e.g., v0.13.7) automatically update the main `basic-memory` formula
-- **Pre-releases** (dev/beta/rc) are NOT automatically updated - users must specify version manually
-- Updates formula in `basicmachines-co/homebrew-basic-memory` repo
-- Requires `HOMEBREW_TOKEN` secret in GitHub repository settings:
-  - Create a fine-grained Personal Access Token with `Contents: Read and Write` and `Actions: Read` scopes on `basicmachines-co/homebrew-basic-memory`
-  - Add as repository secret named `HOMEBREW_TOKEN` in `basicmachines-co/basic-memory`
-- Formula updates include new version URL and SHA256 checksum
-
-### For Development
-- **Automated releases**: Use `just release v0.13.x` for stable releases and `just beta v0.13.0b1` for beta releases
-- **Quality gates**: All releases require passing lint, format, type-check, and test suites
-- **Version management**: Versions automatically derived from git tags via `uv-dynamic-versioning`
-- **Configuration**: `pyproject.toml` uses `dynamic = ["version"]`
-- **Release automation**: `__init__.py` updated automatically during release process
-- **CI/CD**: GitHub Actions handles building and PyPI publication
-
-## Development Notes
-- make sure you sign off on commits
+This level of integration represents a new paradigm in AI-human collaboration, where the AI assistant becomes a full-fledged team member rather than just a tool for generating code snippets.

Dockerfile

@@ -1,5 +1,9 @@
 FROM python:3.12-slim-bookworm
 
+# Build arguments for user ID and group ID (defaults to 1000)
+ARG UID=1000
+ARG GID=1000
+
 # Copy uv from official image
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
@@ -7,6 +11,11 @@ COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 ENV PYTHONUNBUFFERED=1 \
     PYTHONDONTWRITEBYTECODE=1
 
+# Create a group and user with the provided UID/GID
+# Check if the GID already exists, if not create appgroup
+RUN (getent group ${GID} || groupadd --gid ${GID} appgroup) && \
+    useradd --uid ${UID} --gid ${GID} --create-home --shell /bin/bash appuser
+
 # Copy the project into the image
 ADD . /app
 
@@ -14,13 +23,17 @@ ADD . /app
 WORKDIR /app
 RUN uv sync --locked
 
-# Create data directory
-RUN mkdir -p /app/data
+# Create necessary directories and set ownership
+RUN mkdir -p /app/data /app/.basic-memory && \
+    chown -R appuser:${GID} /app
 
 # Set default data directory and add venv to PATH
 ENV BASIC_MEMORY_HOME=/app/data \
     PATH="/app/.venv/bin:$PATH"
 
+# Switch to the non-root user
+USER appuser
+
 # Expose port
 EXPOSE 8000
 

LEGAL_INVENTORY_GUIDE.md

@@ -0,0 +1,250 @@
+# Legal File Inventory Guide
+
+## Overview
+
+This guide documents the comprehensive file inventory script created for Basic Memory's legal documentation needs, including copyright assignments and company agreement exhibits.
+
+## Repository Analysis Summary
+
+### Repository Structure
+- **Primary Language**: Python (3,958 files)
+- **License**: GNU Affero General Public License v3.0
+- **Total Contributors**: 12 identified contributors
+- **Main Contributors**:
+  - `phernandez@basicmachines.co` / `paul@basicmachines.co` (Paul Hernandez) - 700+ commits
+  - `groksrc@gmail.com` / `groksrc@users.noreply.github.com` (Drew Cain) - 18+ commits
+  - Various AI bots and automated systems
+
+### File Type Distribution
+Based on the analysis, the repository contains:
+
+| Extension | Count | Purpose |
+|-----------|-------|---------|
+| `.py` | 3,958 | Python source code |
+| `.pyi` | 4,536 | Python type stubs (dependencies) |
+| `.pyc` | 1,435 | Compiled Python (excluded from inventory) |
+| `.md` | 34 | Documentation files |
+| `.toml` | 179 | Configuration files |
+| `.html` | 119 | Coverage reports and documentation |
+| `.txt` | 127 | Various text files |
+
+### Contributors by Email Domain
+
+**Basic Machines Contributors:**
+- `phernandez@basicmachines.co` - 547 commits (Primary maintainer)
+- `paul@basicmachines.co` / `paulmh@gmail.com` - 170 commits (Paul Hernandez)
+- `claude@basicmachines.co` - 3 commits (AI assistant)
+
+**External Contributors:**
+- `groksrc@gmail.com` / `groksrc@users.noreply.github.com` - 18 commits (Drew Cain)
+- Various one-time contributors (1-2 commits each)
+
+**Automated Systems:**
+- GitHub Actions, semantic-release, and other bots
+
+## Legal Inventory Script Features
+
+### What It Includes
+
+**Source Files:**
+- All Python source code (`.py` files)
+- Configuration files (`.toml`, `.yaml`, `.json`, etc.)
+- Documentation (`.md`, `.rst`, `.txt`)
+- Build and deployment scripts
+- Database migrations and SQL files
+- Legal and license files
+
+**Metadata for Each File:**
+- File path, size, and creation/modification dates
+- Git history (creation date, last modified, commit count)
+- Contributors and their line contributions
+- Primary author identification
+- File categorization
+- SHA-256 hash for integrity verification
+
+### What It Excludes
+
+**Generated/Build Artifacts:**
+- `__pycache__/` and `.pyc` files
+- Build directories (`build/`, `dist/`, `htmlcov/`)
+- Coverage reports and cache files
+
+**Dependencies:**
+- Virtual environment files (`.venv/`, `venv/`)
+- Third-party packages (`site-packages/`, `*.dist-info/`)
+- Lock files (`uv.lock`, `package-lock.json`)
+
+**IDE/Editor Files:**
+- `.idea/`, `.vscode/`, `.DS_Store`
+- Temporary and swap files
+
+**Version Control:**
+- `.git/` directory contents
+- Git configuration files
+
+## Usage Instructions
+
+### Basic Usage
+
+```bash
+# Generate CSV inventory (default)
+python3 legal_file_inventory.py
+
+# Generate Markdown report
+python3 legal_file_inventory.py --format markdown --output legal_report.md
+
+# Generate JSON with full metadata
+python3 legal_file_inventory.py --format json --output legal_data.json
+
+# Specify different repository path
+python3 legal_file_inventory.py --repo-path /path/to/repo --output inventory.csv
+```
+
+### Command Line Options
+
+- `--output`, `-o`: Output file path (default: `basic_memory_legal_inventory.csv`)
+- `--format`, `-f`: Output format - `csv`, `json`, or `markdown` (default: `csv`)
+- `--repo-path`, `-r`: Repository path (default: current directory)
+
+### Output Formats
+
+**CSV Format:**
+- Suitable for spreadsheet applications
+- Contains all metadata fields
+- Contributors stored as JSON string in separate column
+
+**JSON Format:**
+- Complete structured data
+- Includes summary statistics and detailed file information
+- Best for programmatic processing
+
+**Markdown Format:**
+- Human-readable report
+- Summary statistics and contributor rankings
+- Detailed table of all files
+
+## Legal Documentation Applications
+
+### Copyright Assignment Use Cases
+
+1. **Contributor Identification**: The script identifies all contributors to each file based on git blame analysis
+2. **Primary Author Recognition**: Determines the primary author of each file (contributor with most lines)
+3. **Contribution Metrics**: Provides line counts and commit counts per contributor
+4. **File Categorization**: Groups files by purpose (source code, documentation, configuration, etc.)
+
+### Company Agreement Exhibits
+
+The inventory provides comprehensive documentation of:
+
+1. **Intellectual Property Scope**: All source code files and their origins
+2. **Contributor Tracking**: Complete list of all individuals who have contributed code
+3. **File Integrity**: SHA-256 hashes for verification of file contents
+4. **Historical Documentation**: Git creation dates and modification history
+
+### Due Diligence Documentation
+
+The script generates data suitable for:
+
+1. **Legal Review**: Comprehensive file listing with contributor information
+2. **IP Audit**: Identification of all copyright holders
+3. **License Compliance**: Verification of file ownership and licensing
+4. **Asset Documentation**: Complete inventory of company code assets
+
+## Integration with Legal Processes
+
+### Recommended Workflow
+
+1. **Generate Inventory**: Run the script to create current file inventory
+2. **Legal Review**: Have legal counsel review the contributor list and file categorization
+3. **Copyright Assignment**: Use contributor data to ensure proper copyright assignments
+4. **Document Attachment**: Include inventory as exhibit in company agreements
+5. **Regular Updates**: Re-run inventory for significant releases or legal milestones
+
+### Key Legal Considerations
+
+**AGPL-3.0 License:**
+- All files are under AGPL-3.0 unless otherwise specified
+- Contributors retain copyright but license under AGPL-3.0 terms
+- Company needs proper copyright assignments for proprietary licensing
+
+**Contributor Rights:**
+- External contributors may retain rights to their contributions
+- Proper contributor license agreements (CLAs) should be in place
+- AI-generated content may have different legal status
+
+**File Categories for Legal Review:**
+- **Source Code**: Core IP, requires copyright assignment
+- **Configuration**: May contain proprietary deployment information
+- **Documentation**: Usually less sensitive but may contain trade secrets
+- **Legal/License**: Critical for compliance verification
+
+## Maintenance and Updates
+
+### When to Regenerate Inventory
+
+- Before major releases
+- During legal document preparation
+- After significant contributor additions
+- For annual compliance reviews
+- During acquisition or investment processes
+
+### Validation Steps
+
+1. Verify contributor email mapping is accurate
+2. Check that file categorization makes sense
+3. Ensure excluded files are appropriate
+4. Review contributor counts against expectations
+5. Validate file hashes for integrity
+
+## Technical Implementation Notes
+
+### Git Integration
+- Uses `git blame --line-porcelain` for detailed contributor analysis
+- Tracks file history with `git log --follow`
+- Handles renamed files and complex git histories
+
+### Performance Considerations
+- Scans repository incrementally to handle large codebases
+- Excludes binary dependencies to reduce processing time
+- Caches git operations where possible
+
+### Error Handling
+- Gracefully handles files not in git
+- Continues processing if individual files fail
+- Provides detailed error reporting
+
+## Security and Privacy
+
+### Data Sensitivity
+- Contains contributor names and email addresses
+- May reveal internal file structure and organization
+- Should be treated as confidential legal documentation
+
+### Recommended Handling
+- Limit access to legal and executive team
+- Store in secure, access-controlled systems
+- Consider redacting contributor emails for external sharing
+- Regular cleanup of generated inventory files
+
+## Troubleshooting
+
+### Common Issues
+
+**Git Not Available:**
+- Ensure git is installed and repository is initialized
+- Check that the script is run from within the repository
+
+**Permission Errors:**
+- Ensure read access to all repository files
+- Check write permissions for output directory
+
+**Large Repository Performance:**
+- Consider running on subsets of files for very large repositories
+- Use `--repo-path` to target specific subdirectories
+
+**Contributor Mapping Issues:**
+- Git usernames may not match real identities
+- Consider post-processing to normalize contributor names
+- Review .mailmap files for git identity consolidation
+
+This comprehensive legal file inventory system provides the foundation for proper intellectual property documentation and legal compliance for the Basic Memory project.

README.md

@@ -13,11 +13,8 @@ Basic Memory lets you build persistent knowledge through natural conversations w
 Claude, while keeping everything in simple Markdown files on your computer. It uses the Model Context Protocol (MCP) to
 enable any compatible LLM to read and write to your local knowledge base.
 
-- Website: https://basicmemory.com
-- Company: https://basicmachines.co
+- Website: https://basicmachines.co
 - Documentation: https://memory.basicmachines.co
-- Discord: https://discord.gg/tyvKNccgqN
-- YouTube: https://www.youtube.com/@basicmachines-co
 
 ## Pick up your conversation right where you left off
 
@@ -33,10 +30,6 @@ https://github.com/user-attachments/assets/a55d8238-8dd0-454a-be4c-8860dbbd0ddc
 # Install with uv (recommended)
 uv tool install basic-memory
 
-# or with Homebrew
-brew tap basicmachines-co/basic-memory
-brew install basic-memory
-
 # Configure Claude Desktop (edit ~/Library/Application Support/Claude/claude_desktop_config.json)
 # Add this to your config:
 {
@@ -68,14 +61,8 @@ Memory for Claude Desktop:
 npx -y @smithery/cli install @basicmachines-co/basic-memory --client claude
 ```
 
-This installs and configures Basic Memory without requiring manual edits to the Claude Desktop configuration file. Note: The Smithery installation uses their hosted MCP server, while your data remains stored locally as Markdown files.
-
-### Add to Cursor
-
-Once you have installed Basic Memory revisit this page for the 1-click installer for Cursor:
-
-[![Install MCP Server](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/install-mcp?name=basic-memory&config=eyJjb21tYW5kIjoiL1VzZXJzL2RyZXcvLmxvY2FsL2Jpbi91dnggYmFzaWMtbWVtb3J5IG1jcCJ9)
-
+This installs and configures Basic Memory without requiring manual edits to the Claude Desktop configuration file. The
+Smithery server hosts the MCP server component, while your data remains stored locally as Markdown files.
 
 ### Glama.ai
 
@@ -166,8 +153,7 @@ The note embeds semantic content and links to other topics via simple Markdown f
 
 3. You see this file on your computer in real time in the current project directory (default `~/$HOME/basic-memory`).
 
-- Realtime sync is enabled by default starting with v0.12.0
-- Project switching during conversations is supported starting with v0.13.0
+- Realtime sync can be enabled via running `basic-memory sync --watch`
 
 4. In a chat with the LLM, you can reference a topic:
 
@@ -225,7 +211,7 @@ title: <Entity title>
 type: <The type of Entity> (e.g. note)
 permalink: <a uri slug>
 
-- <optional metadata> (such as tags)
+- <optional metadata> (such as tags) 
 ```
 
 ### Observations
@@ -277,13 +263,6 @@ Examples of relations:
 ```
 
 ## Using with VS Code
-For one-click installation, click one of the install buttons below...
-
-[![Install with UV in VS Code](https://img.shields.io/badge/VS_Code-UV-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D) [![Install with UV in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-UV-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D&quality=insiders)
-
-You can use Basic Memory with VS Code to easily retrieve and store information while coding. Click the installation buttons above for one-click setup, or follow the manual installation instructions below.
-
-### Manual Installation
 
 Add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open User Settings (JSON)`.
 
@@ -313,6 +292,8 @@ Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace
 }
 ```
 
+You can use Basic Memory with VS Code to easily retrieve and store information while coding.
+
 ## Using with Claude Desktop
 
 Basic Memory is built using the MCP (Model Context Protocol) and works with the Claude desktop app (https://claude.ai/):
@@ -336,8 +317,7 @@ for OS X):
 }
 ```
 
-If you want to use a specific project (see [Multiple Projects](docs/User%20Guide.md#multiple-projects)), update your
-Claude Desktop
+If you want to use a specific project (see [Multiple Projects](#multiple-projects) below), update your Claude Desktop
 config:
 
 ```json
@@ -347,9 +327,9 @@ config:
       "command": "uvx",
       "args": [
         "basic-memory",
+        "mcp",
         "--project",
-        "your-project-name",
-        "mcp"
+        "your-project-name"
       ]
     }
   }
@@ -358,27 +338,23 @@ config:
 
 2. Sync your knowledge:
 
-Basic Memory will sync the files in your project in real time if you make manual edits.
+```bash
+# One-time sync of local knowledge updates
+basic-memory sync
+
+# Run realtime sync process (recommended)
+basic-memory sync --watch
+```
 
 3. In Claude Desktop, the LLM can now use these tools:
 
 ```
 write_note(title, content, folder, tags) - Create or update notes
 read_note(identifier, page, page_size) - Read notes by title or permalink
-edit_note(identifier, operation, content) - Edit notes incrementally (append, prepend, find/replace)
-move_note(identifier, destination_path) - Move notes with database consistency
-view_note(identifier) - Display notes as formatted artifacts for better readability
 build_context(url, depth, timeframe) - Navigate knowledge graph via memory:// URLs
-search_notes(query, page, page_size) - Search across your knowledge base
+search(query, page, page_size) - Search across your knowledge base
 recent_activity(type, depth, timeframe) - Find recently updated information
 canvas(nodes, edges, title, folder) - Generate knowledge visualizations
-list_memory_projects() - List all available projects with status
-switch_project(project_name) - Switch to different project context
-get_current_project() - Show current project and statistics
-create_memory_project(name, path, set_default) - Create new projects
-delete_project(name) - Delete projects from configuration
-set_default_project(name) - Set default project
-sync_status() - Check file synchronization status
 ```
 
 5. Example prompts to try:
@@ -389,10 +365,6 @@ sync_status() - Check file synchronization status
 "Create a canvas visualization of my project components"
 "Read my notes on the authentication system"
 "What have I been working on in the past week?"
-"Switch to my work-notes project"
-"List all my available projects"
-"Edit my coffee brewing note to add a new technique"
-"Move my old meeting notes to the archive folder"
 ```
 
 ## Futher info
@@ -404,49 +376,6 @@ See the [Documentation](https://memory.basicmachines.co/) for more info, includi
 - [Managing multiple Projects](https://memory.basicmachines.co/docs/cli-reference#project)
 - [Importing data from OpenAI/Claude Projects](https://memory.basicmachines.co/docs/cli-reference#import)
 
-## Installation Options
-
-### Stable Release
-```bash
-pip install basic-memory
-```
-
-### Beta/Pre-releases
-```bash
-pip install basic-memory --pre
-```
-
-### Development Builds
-Development versions are automatically published on every commit to main with versions like `0.12.4.dev26+468a22f`:
-```bash
-pip install basic-memory --pre --force-reinstall
-```
-
-### Docker
-
-Run Basic Memory in a container with volume mounting for your Obsidian vault:
-
-```bash
-# Clone and start with Docker Compose
-git clone https://github.com/basicmachines-co/basic-memory.git
-cd basic-memory
-
-# Edit docker-compose.yml to point to your Obsidian vault
-# Then start the container
-docker-compose up -d
-```
-
-Or use Docker directly:
-```bash
-docker run -d \
-  --name basic-memory-server \
-  -v /path/to/your/obsidian-vault:/data/knowledge:rw \
-  -v basic-memory-config:/root/.basic-memory:rw \
-  ghcr.io/basicmachines-co/basic-memory:latest
-```
-
-See [Docker Setup Guide](docs/Docker.md) for detailed configuration options, multiple project setup, and integration examples.
-
 ## License
 
 AGPL-3.0
@@ -464,4 +393,4 @@ and submitting PRs.
  </picture>
 </a>
 
-Built with ♥️ by Basic Machines
+Built with ♥️ by Basic Machines

create_csv_exhibits.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python3
+"""
+Create CSV exhibits for individual contributors
+"""
+
+import json
+import csv
+from pathlib import Path
+
+def create_csv_exhibits():
+    """Create CSV Exhibit A files for each contributor."""
+    
+    # Read the JSON inventory
+    inventory_files = list(Path("legal_inventory_main").glob("*.json"))
+    if not inventory_files:
+        print("Error: No JSON inventory files found")
+        return
+    
+    inventory_file = inventory_files[0]  # Use the most recent one
+    print(f"Using inventory file: {inventory_file}")
+    
+    with open(inventory_file, 'r') as f:
+        data = json.load(f)
+    
+    files = data['files']
+    
+    # Create output directory
+    output_dir = Path("legal_exhibits")
+    output_dir.mkdir(exist_ok=True)
+    
+    # Contributors we need exhibits for
+    target_contributors = {
+        'jope-bm': 'joe_exhibit_a.csv',
+        'Drew Cain': 'drew_cain_exhibit_a.csv'
+    }
+    
+    print("Creating CSV exhibits for contributors...")
+    
+    for contributor_key, filename in target_contributors.items():
+        # Find files for this contributor
+        contributor_files = []
+        
+        for file_info in files:
+            # Check if this contributor is listed in the file's contributors
+            for contrib in file_info.get('contributors', []):
+                if contributor_key in contrib['name']:
+                    contributor_files.append(file_info)
+                    break
+        
+        if not contributor_files:
+            print(f"No files found for {contributor_key}")
+            continue
+        
+        # Sort files by path
+        contributor_files.sort(key=lambda x: x['path'])
+        
+        # Create CSV file
+        csv_file = output_dir / filename
+        
+        with open(csv_file, 'w', newline='', encoding='utf-8') as csvfile:
+            fieldnames = [
+                'file_path', 'file_name', 'category', 'size_bytes', 
+                'modified_date', 'primary_author', 'all_contributors', 'sha256_hash'
+            ]
+            
+            writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
+            writer.writeheader()
+            
+            for file_info in contributor_files:
+                contributors_list = '; '.join([c['name'] for c in file_info['contributors']])
+                
+                writer.writerow({
+                    'file_path': file_info['path'],
+                    'file_name': file_info['name'],
+                    'category': file_info['category'],
+                    'size_bytes': file_info['size_bytes'],
+                    'modified_date': file_info['modified_time'][:10],
+                    'primary_author': file_info['primary_author'],
+                    'all_contributors': contributors_list,
+                    'sha256_hash': file_info['sha256_hash']
+                })
+        
+        print(f"Created CSV exhibit for {contributor_key}: {csv_file}")
+        print(f"  - {len(contributor_files)} files")
+        print(f"  - {sum(f['size_bytes'] for f in contributor_files):,} bytes")
+
+if __name__ == '__main__':
+    create_csv_exhibits()

create_individual_exhibits.py

@@ -0,0 +1,208 @@
+#!/usr/bin/env python3
+"""
+Create individual Exhibit A files for copyright assignments
+"""
+
+import json
+from pathlib import Path
+from datetime import datetime
+
+def create_individual_exhibits():
+    """Create individual Exhibit A files for each contributor."""
+    
+    # Read the JSON inventory
+    inventory_file = Path("legal_inventory_main/basic_memory_inventory_20250730_101521.json")
+    
+    if not inventory_file.exists():
+        print(f"Error: {inventory_file} not found")
+        return
+    
+    with open(inventory_file, 'r') as f:
+        data = json.load(f)
+    
+    files = data['files']
+    
+    # Create output directory
+    output_dir = Path("legal_exhibits")
+    output_dir.mkdir(exist_ok=True)
+    
+    # Contributors we need exhibits for (based on copyright assignments)
+    target_contributors = {
+        'jope-bm': 'Joseph "Joe" [Last Name]',  # Need to get his full name
+        'Drew Cain': 'Drew Cain'
+    }
+    
+    print("Creating individual contributor exhibits...")
+    
+    for contributor_key, full_name in target_contributors.items():
+        # Find files for this contributor
+        contributor_files = []
+        
+        for file_info in files:
+            # Check if this contributor is listed in the file's contributors
+            for contrib in file_info.get('contributors', []):
+                if contributor_key in contrib['name']:
+                    contributor_files.append(file_info)
+                    break
+        
+        if not contributor_files:
+            print(f"No files found for {contributor_key}")
+            continue
+        
+        # Sort files by path
+        contributor_files.sort(key=lambda x: x['path'])
+        
+        # Create exhibit markdown
+        exhibit_content = f"""# Exhibit A - Assigned Works
+## Copyright Assignment: {full_name} to Basic Memory LLC
+
+**Date:** [To be filled]
+**Assignor:** {full_name}
+**Assignee:** Basic Memory LLC
+
+## Summary
+- **Total Files:** {len(contributor_files)}
+- **Total Size:** {sum(f['size_bytes'] for f in contributor_files):,} bytes
+- **Categories:** {', '.join(set(f['category'] for f in contributor_files))}
+
+## Detailed File List
+
+"""
+        
+        # Group by category
+        categories = {}
+        for file_info in contributor_files:
+            category = file_info['category']
+            if category not in categories:
+                categories[category] = []
+            categories[category].append(file_info)
+        
+        # Add files by category
+        for category, category_files in sorted(categories.items()):
+            exhibit_content += f"### {category.replace('_', ' ').title()}\n\n"
+            
+            for file_info in category_files:
+                exhibit_content += f"**{file_info['path']}**\n"
+                exhibit_content += f"- Size: {file_info['size_bytes']:,} bytes\n"
+                exhibit_content += f"- Modified: {file_info['modified_time'][:10]}\n"
+                exhibit_content += f"- Primary Author: {file_info['primary_author']}\n"
+                
+                # Show all contributors for this file
+                if len(file_info['contributors']) > 1:
+                    contributors_list = ', '.join([c['name'] for c in file_info['contributors']])
+                    exhibit_content += f"- All Contributors: {contributors_list}\n"
+                
+                exhibit_content += f"- SHA-256: `{file_info['sha256_hash']}`\n\n"
+        
+        # Add verification section
+        exhibit_content += f"""
+## Verification
+This exhibit lists all files in the Basic Memory repository where {full_name} is identified as a contributor based on git commit history analysis.
+
+**Analysis Date:** {datetime.now().strftime('%Y-%m-%d')}
+**Repository State:** Basic Memory main branch
+**Method:** Git history analysis via `git log --follow` for each file
+
+## Legal Representation
+{full_name} hereby represents and warrants that they are the author of the contributions listed above and have the right to assign copyright in these works to Basic Memory LLC.
+
+---
+
+*This exhibit is attached to and forms part of the Copyright Assignment Agreement between {full_name} and Basic Memory LLC.*
+"""
+        
+        # Write exhibit file
+        safe_name = contributor_key.replace(' ', '_').replace('-', '_').lower()
+        exhibit_file = output_dir / f"exhibit_a_{safe_name}.md"
+        
+        with open(exhibit_file, 'w') as f:
+            f.write(exhibit_content)
+        
+        print(f"Created exhibit for {full_name}: {exhibit_file}")
+        print(f"  - {len(contributor_files)} files")
+        print(f"  - {sum(f['size_bytes'] for f in contributor_files):,} bytes")
+    
+    # Create overall summary exhibit (for Paul's assignment to Basic Machines LLC)
+    create_overall_summary_exhibit(data, output_dir)
+
+def create_overall_summary_exhibit(data, output_dir):
+    """Create overall summary exhibit for Company Agreement."""
+    
+    files = data['files']
+    summary = data['summary']
+    contributors = data['contributors']
+    
+    summary_content = f"""# Basic Memory Repository - Complete IP Inventory
+## For Basic Memory LLC Company Agreement
+
+**Analysis Date:** {summary['scan_date'][:10]}
+**Repository:** {summary['repository_path']}
+
+## Executive Summary
+- **Total Files:** {summary['total_files']:,}
+- **Total Size:** {summary['total_size_bytes']:,} bytes
+- **Contributors:** {summary['contributor_count']}
+- **Primary Author:** Paul Hernandez ({len(contributors.get('Paul Hernandez', {}).get('files', []))} files)
+
+## File Categories
+"""
+    
+    for category, count in sorted(summary['categories'].items()):
+        summary_content += f"- **{category.replace('_', ' ').title()}:** {count} files\n"
+    
+    summary_content += """
+
+## Contributor Summary
+"""
+    
+    for contrib in summary['top_contributors']:
+        summary_content += f"- **{contrib['name']}** ({contrib['email']}): {contrib['file_count']} files, {contrib['commit_count']} commits\n"
+    
+    summary_content += """
+
+## Legal Significance
+This inventory represents the complete codebase of Basic Memory as licensed from Basic Machines LLC to Basic Memory LLC under the copyright license agreement dated [DATE].
+
+### IP Rights Chain
+1. **Paul Hernandez** → Basic Machines LLC (copyright assignment)
+2. **Basic Machines LLC** → Basic Memory LLC (15% royalty license)
+3. **Co-founders** → Basic Memory LLC (direct copyright assignments)
+
+### Due Diligence Documentation
+This comprehensive file inventory serves as:
+- **Company Agreement Exhibit:** Original codebase licensed to Basic Memory LLC
+- **Acquisition Documentation:** Complete IP inventory for due diligence
+- **Copyright Verification:** Establishes chain of title for all repository contents
+
+## Repository Contents by Category
+
+"""
+    
+    # Add sample files by category (first 10 in each category)
+    for category in sorted(summary['categories'].keys()):
+        category_files = [f for f in files if f['category'] == category][:10]
+        if category_files:
+            summary_content += f"### {category.replace('_', ' ').title()} (Sample)\n\n"
+            for file_info in category_files:
+                summary_content += f"- `{file_info['path']}` ({file_info['size_bytes']:,} bytes)\n"
+            
+            if len([f for f in files if f['category'] == category]) > 10:
+                remaining = len([f for f in files if f['category'] == category]) - 10
+                summary_content += f"- *... and {remaining} more files*\n"
+            summary_content += "\n"
+    
+    summary_content += f"""
+---
+
+*This inventory was generated automatically from git repository analysis and represents the complete intellectual property foundation of Basic Memory as of {summary['scan_date'][:10]}.*
+"""
+    
+    # Write summary file
+    summary_file = output_dir / "basic_memory_complete_inventory.md"
+    with open(summary_file, 'w') as f:
+        f.write(summary_content)
+    
+    print(f"Created complete inventory summary: {summary_file}")
+
+if __name__ == '__main__':
+    create_individual_exhibits()

docs/Docker.md

@@ -15,7 +15,7 @@ Basic Memory provides pre-built Docker images on GitHub Container Registry that
      --name basic-memory-server \
      -p 8000:8000 \
      -v /path/to/your/obsidian-vault:/app/data:rw \
-     -v basic-memory-config:/root/.basic-memory:rw \
+     -v basic-memory-config:/app/.basic-memory:rw \
      ghcr.io/basicmachines-co/basic-memory:latest
    ```
 
@@ -30,7 +30,7 @@ Basic Memory provides pre-built Docker images on GitHub Container Registry that
          - "8000:8000"
        volumes:
          - /path/to/your/obsidian-vault:/app/data:rw
-         - basic-memory-config:/root/.basic-memory:rw
+         - basic-memory-config:/app/.basic-memory:rw
        environment:
          - BASIC_MEMORY_DEFAULT_PROJECT=main
        restart: unless-stopped
@@ -67,7 +67,7 @@ docker build -t basic-memory .
 docker run -d \
   --name basic-memory-server \
   -v /path/to/your/obsidian-vault:/app/data:rw \
-  -v basic-memory-config:/root/.basic-memory:rw \
+  -v basic-memory-config:/app/.basic-memory:rw \
   -e BASIC_MEMORY_DEFAULT_PROJECT=main \
   basic-memory
 ```
@@ -86,11 +86,11 @@ Basic Memory requires several volume mounts for proper operation:
 
 2. **Configuration and Database** (Recommended):
    ```yaml
-   - basic-memory-config:/root/.basic-memory:rw
+   - basic-memory-config:/app/.basic-memory:rw
    ```
    Persistent storage for configuration and SQLite database.
 
-You can edit the basic-memory config.json file located in the /root/.basic-memory/config.json after Basic Memory starts.
+You can edit the basic-memory config.json file located in the /app/.basic-memory/config.json after Basic Memory starts.
 
 3. **Multiple Projects** (Optional):
    ```yaml
@@ -98,7 +98,7 @@ You can edit the basic-memory config.json file located in the /root/.basic-memor
    - /path/to/project2:/app/data/project2:rw
    ```
 
-You can edit the basic-memory config.json file located in the /root/.basic-memory/config.json
+You can edit the basic-memory config.json file located in the /app/.basic-memory/config.json
 
 ## CLI Commands via Docker
 
@@ -123,7 +123,7 @@ When using Docker volumes, you'll need to configure projects to point to your mo
 
 1. **Check current configuration:**
    ```bash
-   docker exec basic-memory-server cat /root/.basic-memory/config.json
+   docker exec basic-memory-server cat /app/.basic-memory/config.json
    ```
 
 2. **Add a project for your mounted volume:**
@@ -184,16 +184,47 @@ environment:
 
 ### Linux/macOS
 
-Ensure your knowledge directories have proper permissions:
+The Docker container now runs as a non-root user to avoid file ownership issues. By default, the container uses UID/GID 1000, but you can customize this to match your user:
 
 ```bash
-# Make directories readable/writable
-chmod -R 755 /path/to/your/obsidian-vault
+# Build with custom UID/GID to match your user
+docker build --build-arg UID=$(id -u) --build-arg GID=$(id -g) -t basic-memory .
 
-# If using specific user/group
-chown -R $USER:$USER /path/to/your/obsidian-vault
+# Or use docker-compose with build args
 ```
 
+**Example docker-compose.yml with custom user:**
+```yaml
+version: '3.8'
+services:
+  basic-memory:
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        UID: 1000  # Replace with your UID
+        GID: 1000  # Replace with your GID
+    container_name: basic-memory-server
+    ports:
+      - "8000:8000"
+    volumes:
+      - /path/to/your/obsidian-vault:/app/data:rw
+      - basic-memory-config:/app/.basic-memory:rw
+    environment:
+      - BASIC_MEMORY_DEFAULT_PROJECT=main
+    restart: unless-stopped
+```
+
+**Using pre-built images:**
+If using the pre-built image from GitHub Container Registry, files will be created with UID/GID 1000. You can either:
+
+1. Change your local directory ownership to match:
+   ```bash
+   sudo chown -R 1000:1000 /path/to/your/obsidian-vault
+   ```
+
+2. Or build your own image with custom UID/GID as shown above.
+
 ### Windows
 
 When using Docker Desktop on Windows, ensure the directories are shared:
@@ -217,7 +248,7 @@ When using Docker Desktop on Windows, ensure the directories are shared:
       ```
 
 2. **Configuration Not Persisting:**
-    - Use named volumes for `/root/.basic-memory`
+    - Use named volumes for `/app/.basic-memory`
     - Check volume mount permissions
 
 3. **Network Connectivity:**
@@ -243,10 +274,10 @@ docker-compose logs -f basic-memory
 ## Security Considerations
 
 1. **Docker Security:**
-   The container runs as root for simplicity. For production, consider additional security measures.
+   The container runs as a non-root user (UID/GID 1000 by default) for improved security. You can customize the user ID using build arguments to match your local user.
 
 2. **Volume Permissions:**
-   Ensure mounted directories have appropriate permissions and don't expose sensitive data.
+   Ensure mounted directories have appropriate permissions and don't expose sensitive data. With the non-root container, files will be created with the specified user ownership.
 
 3. **Network Security:**
    If using HTTP transport, consider using reverse proxy with SSL/TLS and authentication if the endpoint is available on
@@ -288,7 +319,7 @@ For Docker-specific issues:
 1. Check the [troubleshooting section](#troubleshooting) above
 2. Review container logs: `docker-compose logs basic-memory`
 3. Verify volume mounts: `docker inspect basic-memory-server`
-4. Test file permissions: `docker exec basic-memory-server ls -la /root`
+4. Test file permissions: `docker exec basic-memory-server ls -la /app`
 
 For general Basic Memory support, see the main [README](../README.md)
 and [documentation](https://memory.basicmachines.co/).

legal_exhibits/drew_cain_exhibit_a.csv

@@ -0,0 +1,31 @@
+file_path,file_name,category,size_bytes,modified_date,primary_author,all_contributors,sha256_hash
+.github/workflows/release.yml,release.yml,configuration,2479,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez,163307a99e2f3d317af6ae8927e1537654d88bf574a6958ac0bcd2d4de266b2a
+CLAUDE.md,CLAUDE.md,legal,12310,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; bm-claudeai (AI Assistant); Ikko Eltociear Ashimine,751f10c1a9a9c0ba2054d9c9cd36cf0989d6a347491fd505bb6504ee74b12900
+README.md,README.md,documentation,16261,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; Jason Noble; Marc Baiza; Matias Forbord; bm-claudeai (AI Assistant),2c4b82b30f49ab465617034fda999157450ed168f8e097fe8e9ca7ac65a197a7
+justfile,justfile,other,5496,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain,a8df6c73ee8cf3eaa48e4cba193dffbc2821b843a8cc0c0cd58b8517f2252907
+pyproject.toml,pyproject.toml,configuration,3279,2025-07-30,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant); semantic-release,428a5d64d4555dc7cd2a81b89a3444bdb1d2f3017257fbc9160bd0ae982718e1
+src/basic_memory/__init__.py,__init__.py,source_code,256,2025-07-06,Paul Hernandez,Paul Hernandez; Drew Cain; semantic-release,c946490ab9d64957d25df37f721392024916f8a81ed838f70a8e938b1c2637db
+src/basic_memory/alembic/env.py,env.py,source_code,2838,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),e241d987eadfcd5011cbd9ddbecb833d306de87937759d81c08d37d04a6906b0
+src/basic_memory/api/routers/utils.py,utils.py,source_code,5159,2025-07-03,Drew Cain,Drew Cain; bm-claudeai (AI Assistant),9e60f57da24e1dc9d64236c26a7a2353003dc618a77fbeb853c494aa3357a57c
+src/basic_memory/cli/commands/mcp.py,mcp.py,source_code,2593,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),3e1be3d27b18ef4743204b7cf8a37fbc2a1a91fc1636c468e08cefcd8597bac6
+src/basic_memory/config.py,config.py,source_code,12487,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant); github-actions[bot] (AI Assistant),86341330a041b94d38f5e4f1b94f3509d74351c67cc826af1a4ff57313e5f726
+src/basic_memory/db.py,db.py,source_code,7428,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),25e053b0b3f9e8fa823b05fc099001efe8a3a4f6e0f80728e5079ba45aa406d8
+src/basic_memory/mcp/server.py,server.py,source_code,1248,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),0a910cae27d61ea923e90fbe2d4b5c7cacf3b29d3e156f0b7f77872ab973c761
+src/basic_memory/mcp/tools/__init__.py,__init__.py,source_code,1619,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez,872b771dd52ec3b763645a2baf6e10a70f049ce3106830a6d3f053b3e09a5fe6
+src/basic_memory/mcp/tools/project_management.py,project_management.py,source_code,12944,2025-07-06,Drew Cain,Drew Cain; Paul Hernandez,cdac736d65129f689a85c6b82f8e043bc84a31657ead7a8331771171eeaa860f
+src/basic_memory/mcp/tools/search.py,search.py,source_code,15883,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; bm-claudeai (AI Assistant); github-actions[bot] (AI Assistant),8519b0057468c4450eb543a2f561bcd0d7cb96e1ce1b95e948e02b309ba6b7ca
+src/basic_memory/repository/entity_repository.py,entity_repository.py,source_code,10405,2025-07-03,Drew Cain,Drew Cain; bm-claudeai (AI Assistant); Paul Hernandez,e2a8d1eba6c8d64bc61d7168df0fe8c29a670858bf9daeac464a0f440273fae0
+src/basic_memory/schemas/memory.py,memory.py,source_code,5833,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; bm-claudeai (AI Assistant),acb4a953a553feca672c4895798a7d948ec51f922f75b66dd7d55716e3bebed3
+src/basic_memory/services/entity_service.py,entity_service.py,source_code,30440,2025-07-03,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant); github-actions[bot] (AI Assistant),7cd5163eca6b8a0772e838c8c869e478166763cd6a2d745b0b9aa5c25a65baee
+src/basic_memory/services/initialization.py,initialization.py,source_code,6715,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),4dde58b799cf4ac90631e59949b55b3355a93bdf99df0d9c2408c0cea67e10c4
+src/basic_memory/templates/prompts/continue_conversation.hbs,continue_conversation.hbs,templates,3076,2025-07-01,Drew Cain,Drew Cain; bm-claudeai (AI Assistant),b6bac31d25c0e52d0909b2273285092f4e31bc219107f92ed511cd407b65e992
+src/basic_memory/utils.py,utils.py,source_code,8654,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain; andyxinweiminicloud; github-actions[bot] (AI Assistant),111f343e3367339730e081c08acf4613667be574f946126513b5d82da3086bed
+tests/mcp/test_tool_edit_note.py,test_tool_edit_note.py,source_code,13503,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez,dd441969aa54b3739f2d9202d3feaf46aee807ec51e01a13ef41eda52743944f
+tests/mcp/test_tool_search.py,test_tool_search.py,source_code,10959,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; github-actions[bot] (AI Assistant),07839cf8e89d74ba05ec1dc55fa842444c1f0cc3d1587823b0ac3458ad89e87c
+tests/mcp/test_tool_write_note.py,test_tool_write_note.py,source_code,35136,2025-07-30,jope-bm,jope-bm; Drew Cain; Paul Hernandez,45172de20cfc4f4436287573b4f5a94b8b616a360647af67ba1c6c343ccd41b8
+tests/repository/test_entity_repository_upsert.py,test_entity_repository_upsert.py,source_code,16983,2025-07-03,Paul Hernandez,Paul Hernandez; Drew Cain,ee0ecd6f4ff8b31838bd6de6fb1018af437e02813d8315c06f4e20a6b78a0572
+tests/schemas/test_schemas.py,test_schemas.py,source_code,16880,2025-07-03,Drew Cain,Drew Cain; Paul Hernandez; bm-claudeai (AI Assistant),2c746a00c340f063c160ace67569955a300a294040949695c79fd4ae124fb611
+tests/services/test_entity_service.py,test_entity_service.py,source_code,59278,2025-07-03,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),d7d495756faa10b415d705cf26b69d2efbc5f190a834b6767386ff296629ea71
+tests/test_config.py,test_config.py,source_code,3680,2025-07-03,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),6a246431cff739274efda895dfa28f38710289a73e645312f5fa05fce0885ec8
+tests/test_db_migration_deduplication.py,test_db_migration_deduplication.py,source_code,6166,2025-07-08,Paul Hernandez,Paul Hernandez; Drew Cain,ab768e061531ca2edcd598c101b5d884e549f90c7a4b305a23713a199d263fbb
+uv.lock,uv.lock,other,232710,2025-07-30,Paul Hernandez,Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant),caa1e3f6e66464b884a78cab77df2fe303fa3c0dc573be0196474b6d3c150581

legal_exhibits/joe_exhibit_a.csv

@@ -0,0 +1,28 @@
+file_path,file_name,category,size_bytes,modified_date,primary_author,all_contributors,sha256_hash
+CONTRIBUTING.md,CONTRIBUTING.md,documentation,7329,2025-07-30,jope-bm,jope-bm; Paul Hernandez,ca822fe39cc529bfc3822d317ab8a20fd141ec3ecb8c20de9e2eca3edce1c282
+justfile,justfile,other,5496,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain,a8df6c73ee8cf3eaa48e4cba193dffbc2821b843a8cc0c0cd58b8517f2252907
+src/basic_memory/api/routers/project_router.py,project_router.py,source_code,8444,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),6539c69f1d506c65d14cc2c151876b19057f37d84d51a9e6f464ed47a4692648
+src/basic_memory/cli/commands/import_memory_json.py,import_memory_json.py,source_code,3013,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),7ea193f6720b2672290ad16c79a143a31d88a1d567838f12b9ebf9110a7c0338
+src/basic_memory/cli/commands/project.py,project.py,source_code,13836,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),af3e6f30410ab48355f4b1a46aaa3aa5423cb0a0490f51447db1d25e09f39916
+src/basic_memory/config.py,config.py,source_code,12487,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain; bm-claudeai (AI Assistant); github-actions[bot] (AI Assistant),86341330a041b94d38f5e4f1b94f3509d74351c67cc826af1a4ff57313e5f726
+src/basic_memory/importers/memory_json_importer.py,memory_json_importer.py,source_code,4631,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),bc7d045299f17ed9ad5cebff7b1423250ec28a11130e47a0ac48d3ab82bdeafc
+src/basic_memory/mcp/async_client.py,async_client.py,source_code,925,2025-07-30,jope-bm,jope-bm; Paul Hernandez,6531f4387f30a30a322197ff51d6eacae4b25a58c648095931b3d1145d1da303
+src/basic_memory/mcp/tools/move_note.py,move_note.py,source_code,17541,2025-07-30,jope-bm,jope-bm; Paul Hernandez,5ef27d9baaebc2c5656fc49c4798a4e4e40a70b6cd9d1e761dbcae021bad558c
+src/basic_memory/mcp/tools/read_content.py,read_content.py,source_code,9125,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),96a13addac507fd874394dfa2e1e5ed71af5eb89d0872c1d68cacf9cac3f8724
+src/basic_memory/mcp/tools/read_note.py,read_note.py,source_code,8132,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant); Amadeusz Wieczorek; github-actions[bot] (AI Assistant),dff53ce02b16d9c5fca315b3f09bb70867a89d614b0ef3f0548dce87978048ee
+src/basic_memory/mcp/tools/write_note.py,write_note.py,source_code,6612,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),771396fb49d397feb5f7e36321d4d233c22c4d1b53414912c849957c6e96fc83
+src/basic_memory/repository/project_repository.py,project_repository.py,source_code,3803,2025-07-30,jope-bm,jope-bm; bm-claudeai (AI Assistant),9083ba214b2bcaaf98164d9c33cda7add52bc77f7269ecb6e43cdd5088728b7c
+src/basic_memory/schemas/importer.py,importer.py,source_code,693,2025-07-30,jope-bm,jope-bm; bm-claudeai (AI Assistant),ac33df423ca32b28ce7b6ea9c29d541f8783a86c0c29f78db35163bf93f139cd
+src/basic_memory/services/project_service.py,project_service.py,source_code,30125,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),bce95c00aa9a1da0a8c8090ee34b5b1494207f8c99e6c25de4ec43fddc38f6be
+src/basic_memory/utils.py,utils.py,source_code,8654,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Drew Cain; andyxinweiminicloud; github-actions[bot] (AI Assistant),111f343e3367339730e081c08acf4613667be574f946126513b5d82da3086bed
+tests/api/test_async_client.py,test_async_client.py,source_code,1382,2025-07-30,jope-bm,jope-bm; Paul Hernandez,a2f96226a75e5cff2326ca48ddccea4915964d83e529f7b99958bc233ccdc31a
+tests/api/test_project_router.py,test_project_router.py,source_code,13288,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),af85d0870069d3831a9214372853994e5d12dc910e37298eb9958f72f6a8bb31
+tests/cli/test_import_memory_json.py,test_import_memory_json.py,source_code,4891,2025-07-30,jope-bm,jope-bm; bm-claudeai (AI Assistant); Paul Hernandez,d6734ce059dacf97bc764d848b2e2a6ba52fa96871bc331ec9d2ddc60b766bb6
+tests/cli/test_project_commands.py,test_project_commands.py,source_code,6578,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),51e2ac7ff44b0d1a1db6da406c5c2e6aebceb1b63a1e8d5ab51bbaa834507157
+tests/mcp/test_tool_move_note.py,test_tool_move_note.py,source_code,25851,2025-07-30,jope-bm,jope-bm; Paul Hernandez,c9f95158503fa42e37532aaa35027538fa49cea718d059d570cf547d31f01043
+tests/mcp/test_tool_read_content.py,test_tool_read_content.py,source_code,19442,2025-07-30,jope-bm,jope-bm,1817e32f997b06dbdabf02864d0c70584c1cd80bf1fae8dfbef649de79434bc5
+tests/mcp/test_tool_read_note.py,test_tool_read_note.py,source_code,22991,2025-07-30,jope-bm,jope-bm; Paul Hernandez; Amadeusz Wieczorek; github-actions[bot] (AI Assistant),4e13ea9ff977525aa62b6a8c22505ffe989329dc3e7d07b71e044cf43ef3ddfd
+tests/mcp/test_tool_write_note.py,test_tool_write_note.py,source_code,35136,2025-07-30,jope-bm,jope-bm; Drew Cain; Paul Hernandez,45172de20cfc4f4436287573b4f5a94b8b616a360647af67ba1c6c343ccd41b8
+tests/repository/test_project_repository.py,test_project_repository.py,source_code,10511,2025-07-30,jope-bm,jope-bm; bm-claudeai (AI Assistant),279a3324635b1b515c18003bd1875cf230fef1192cadef9ca426846783717e75
+tests/services/test_project_service.py,test_project_service.py,source_code,28152,2025-07-30,jope-bm,jope-bm; Paul Hernandez; bm-claudeai (AI Assistant),430868ed796518937a3b0bed4d8c33be53264a6100d61d54b0745bb2b58bf29a
+tests/utils/test_validate_project_path.py,test_validate_project_path.py,source_code,15346,2025-07-30,jope-bm,jope-bm,27a4bf2a9d277e6cd773619e5241b20175d211ec60c284361bec404fd99143f3

legal_file_inventory.py

@@ -0,0 +1,438 @@
+#!/usr/bin/env python3
+"""
+Legal File Inventory Generator for Basic Memory
+
+This script generates a comprehensive file inventory for legal documentation purposes,
+including copyright assignments and company agreement exhibits.
+
+The inventory includes:
+- All source code files and their contributors
+- Documentation and configuration files
+- License and legal files
+- Excludes generated files, dependencies, and temporary files
+
+Usage:
+    python legal_file_inventory.py [--output inventory.csv] [--format csv|json|markdown]
+"""
+
+import os
+import json
+import csv
+import subprocess
+from pathlib import Path
+from datetime import datetime
+from typing import Dict, List
+import argparse
+import hashlib
+
+class FileInventoryGenerator:
+    def __init__(self, repo_path: str = "."):
+        self.repo_path = Path(repo_path).resolve()
+        self.inventory = []
+        
+        # File patterns to exclude from legal inventory
+        self.exclude_patterns = {
+            # Version control and git
+            '.git', '.gitignore', '.gitmodules',
+            
+            # Python compiled and cache files
+            '__pycache__', '*.pyc', '*.pyo', '*.pyd', '.pytest_cache',
+            
+            # Virtual environments and dependencies
+            '.venv', 'venv', '.env', 'env', 'ENV',
+            '*.dist-info', 'site-packages',
+            
+            # IDE and editor files
+            '.idea', '.vscode', '*.swp', '*.swo', '.DS_Store',
+            
+            # Build and distribution artifacts
+            'build', 'dist', 'htmlcov', '.coverage', '.coverage.*',
+            '*.egg-info', '.eggs', 'wheels',
+            
+            # Cache and temporary files
+            '.ruff_cache', '.mypy_cache', '.tox',
+            'node_modules', '.npm',
+            
+            # Documentation build artifacts (but keep source docs)
+            '.obsidian',
+            
+            # Lock files (these are generated)
+            'uv.lock', 'Pipfile.lock', 'poetry.lock', 'package-lock.json'
+        }
+        
+        # File extensions that are definitely source/authored content
+        self.source_extensions = {
+            '.py', '.md', '.rst', '.txt', '.toml', '.yaml', '.yml',
+            '.json', '.cfg', '.ini', '.conf', '.sh', '.sql',
+            '.js', '.ts', '.jsx', '.tsx', '.css', '.scss', '.sass',
+            '.html', '.htm', '.xml', '.svg', '.dockerfile', '.Dockerfile'
+        }
+        
+        # License file patterns
+        self.license_patterns = {
+            'LICENSE', 'LICENCE', 'COPYING', 'COPYRIGHT',
+            'license.txt', 'LICENSE.txt', 'LICENSE.md',
+            'CITATION.cff', 'CLA.md'
+        }
+
+    def run_git_command(self, command: List[str]) -> str:
+        """Run a git command and return the output."""
+        try:
+            result = subprocess.run(
+                ['git'] + command,
+                cwd=self.repo_path,
+                capture_output=True,
+                text=True,
+                check=True
+            )
+            return result.stdout.strip()
+        except subprocess.CalledProcessError:
+            return ""
+
+    def get_file_contributors(self, file_path: str) -> Dict[str, int]:
+        """Get contributors and their line contributions for a file."""
+        try:
+            blame_output = self.run_git_command(['blame', '--line-porcelain', file_path])
+            contributors = {}
+            
+            for line in blame_output.split('\n'):
+                if line.startswith('author '):
+                    author = line[7:]  # Remove 'author ' prefix
+                    contributors[author] = contributors.get(author, 0) + 1
+                    
+            return contributors
+        except Exception:
+            return {}
+
+    def get_file_history(self, file_path: str) -> Dict[str, any]:
+        """Get file creation date, last modification, and total commits."""
+        try:
+            # Get creation date (first commit)
+            first_commit = self.run_git_command([
+                'log', '--follow', '--format=%ad', '--date=iso',
+                '--reverse', file_path
+            ]).split('\n')[0] if self.run_git_command([
+                'log', '--follow', '--format=%ad', '--date=iso', 
+                '--reverse', file_path
+            ]) else None
+            
+            # Get last modification date
+            last_commit = self.run_git_command([
+                'log', '-1', '--format=%ad', '--date=iso', file_path
+            ])
+            
+            # Get total commits for this file
+            commit_count = len(self.run_git_command([
+                'log', '--follow', '--oneline', file_path
+            ]).split('\n')) if self.run_git_command([
+                'log', '--follow', '--oneline', file_path
+            ]) else 0
+            
+            return {
+                'created': first_commit or 'Unknown',
+                'last_modified': last_commit or 'Unknown',
+                'commit_count': commit_count
+            }
+        except Exception:
+            return {
+                'created': 'Unknown',
+                'last_modified': 'Unknown', 
+                'commit_count': 0
+            }
+
+    def should_exclude_file(self, file_path: Path) -> bool:
+        """Determine if a file should be excluded from the inventory."""
+        str_path = str(file_path)
+        
+        # Check if any part of the path matches exclude patterns
+        for pattern in self.exclude_patterns:
+            if pattern in str_path or file_path.match(pattern):
+                return True
+        
+        # Exclude files in virtual environment paths
+        if '/.venv/' in str_path or '/venv/' in str_path:
+            return True
+            
+        # Exclude binary files that are likely dependencies
+        if file_path.suffix in {'.so', '.dylib', '.dll', '.pyd'}:
+            return True
+            
+        return False
+
+    def calculate_file_hash(self, file_path: Path) -> str:
+        """Calculate SHA-256 hash of file content."""
+        try:
+            with open(file_path, 'rb') as f:
+                return hashlib.sha256(f.read()).hexdigest()
+        except Exception:
+            return ""
+
+    def categorize_file(self, file_path: Path) -> str:
+        """Categorize the file based on its path and extension."""
+        str_path = str(file_path).lower()
+        
+        # License and legal files
+        if any(pattern.lower() in file_path.name.lower() for pattern in self.license_patterns):
+            return "Legal/License"
+        
+        # Documentation
+        if file_path.suffix.lower() in {'.md', '.rst', '.txt'} and any(
+            doc_dir in str_path for doc_dir in ['doc', 'readme', 'changelog', 'contributing']
+        ):
+            return "Documentation"
+        
+        # Configuration files
+        if file_path.suffix.lower() in {'.toml', '.yaml', '.yml', '.json', '.cfg', '.ini', '.conf'}:
+            return "Configuration"
+        
+        # Source code
+        if file_path.suffix.lower() in {'.py', '.js', '.ts', '.jsx', '.tsx'}:
+            return "Source Code"
+        
+        # Tests
+        if 'test' in str_path and file_path.suffix.lower() == '.py':
+            return "Test Code"
+        
+        # Build and deployment
+        if file_path.name.lower() in {'dockerfile', 'justfile', 'makefile'} or file_path.suffix.lower() in {'.sh'}:
+            return "Build/Deployment"
+        
+        # Database and migrations
+        if 'migration' in str_path or 'alembic' in str_path or file_path.suffix.lower() == '.sql':
+            return "Database/Migration"
+        
+        # Templates and resources
+        if file_path.suffix.lower() in {'.hbs', '.j2', '.jinja', '.template'}:
+            return "Templates/Resources"
+        
+        return "Other"
+
+    def scan_repository(self):
+        """Scan the repository and build the file inventory."""
+        print(f"Scanning repository: {self.repo_path}")
+        
+        for root, dirs, files in os.walk(self.repo_path):
+            # Skip excluded directories
+            dirs[:] = [d for d in dirs if not any(pattern in d for pattern in self.exclude_patterns)]
+            
+            for file in files:
+                file_path = Path(root) / file
+                relative_path = file_path.relative_to(self.repo_path)
+                
+                # Skip excluded files
+                if self.should_exclude_file(relative_path):
+                    continue
+                
+                # Get file stats
+                try:
+                    stat_info = file_path.stat()
+                    file_size = stat_info.st_size
+                    modified_time = datetime.fromtimestamp(stat_info.st_mtime)
+                except Exception:
+                    file_size = 0
+                    modified_time = datetime.now()
+                
+                # Get git information
+                contributors = self.get_file_contributors(str(relative_path))
+                history = self.get_file_history(str(relative_path))
+                
+                # Calculate file hash for integrity verification
+                file_hash = self.calculate_file_hash(file_path)
+                
+                # Build inventory entry
+                entry = {
+                    'file_path': str(relative_path),
+                    'full_path': str(file_path),
+                    'file_name': file_path.name,
+                    'file_extension': file_path.suffix,
+                    'file_size_bytes': file_size,
+                    'category': self.categorize_file(relative_path),
+                    'fs_modified_date': modified_time.isoformat(),
+                    'git_created_date': history['created'],
+                    'git_last_modified': history['last_modified'],
+                    'git_commit_count': history['commit_count'],
+                    'contributors': contributors,
+                    'primary_author': max(contributors.items(), key=lambda x: x[1])[0] if contributors else 'Unknown',
+                    'contributor_count': len(contributors),
+                    'total_author_lines': sum(contributors.values()) if contributors else 0,
+                    'sha256_hash': file_hash,
+                    'scan_timestamp': datetime.now().isoformat()
+                }
+                
+                self.inventory.append(entry)
+        
+        print(f"Scanned {len(self.inventory)} files")
+
+    def get_summary_statistics(self) -> Dict:
+        """Generate summary statistics for the inventory."""
+        if not self.inventory:
+            return {}
+        
+        # Collect all contributors
+        all_contributors = set()
+        for entry in self.inventory:
+            all_contributors.update(entry['contributors'].keys())
+        
+        # Category breakdown
+        categories = {}
+        for entry in self.inventory:
+            cat = entry['category']
+            categories[cat] = categories.get(cat, 0) + 1
+        
+        # File extension breakdown
+        extensions = {}
+        for entry in self.inventory:
+            ext = entry['file_extension'] or 'no_extension'
+            extensions[ext] = extensions.get(ext, 0) + 1
+        
+        # Contributor statistics
+        contributor_files = {}
+        contributor_lines = {}
+        for entry in self.inventory:
+            for contributor, lines in entry['contributors'].items():
+                contributor_files[contributor] = contributor_files.get(contributor, 0) + 1
+                contributor_lines[contributor] = contributor_lines.get(contributor, 0) + lines
+        
+        return {
+            'total_files': len(self.inventory),
+            'total_contributors': len(all_contributors),
+            'categories': categories,
+            'file_extensions': extensions,
+            'contributor_file_counts': contributor_files,
+            'contributor_line_counts': contributor_lines,
+            'scan_date': datetime.now().isoformat(),
+            'repository_path': str(self.repo_path)
+        }
+
+    def export_csv(self, output_file: str):
+        """Export inventory to CSV format."""
+        with open(output_file, 'w', newline='', encoding='utf-8') as f:
+            if not self.inventory:
+                return
+            
+            fieldnames = list(self.inventory[0].keys())
+            # Convert complex fields to strings for CSV
+            fieldnames = [f for f in fieldnames if f != 'contributors']
+            fieldnames.append('contributors_json')
+            
+            writer = csv.DictWriter(f, fieldnames=fieldnames)
+            writer.writeheader()
+            
+            for entry in self.inventory:
+                row = {k: v for k, v in entry.items() if k != 'contributors'}
+                row['contributors_json'] = json.dumps(entry['contributors'])
+                writer.writerow(row)
+
+    def export_json(self, output_file: str):
+        """Export inventory to JSON format."""
+        export_data = {
+            'metadata': self.get_summary_statistics(),
+            'files': self.inventory
+        }
+        
+        with open(output_file, 'w', encoding='utf-8') as f:
+            json.dump(export_data, f, indent=2, ensure_ascii=False)
+
+    def export_markdown(self, output_file: str):
+        """Export inventory to Markdown format."""
+        stats = self.get_summary_statistics()
+        
+        with open(output_file, 'w', encoding='utf-8') as f:
+            f.write("# Basic Memory - Legal File Inventory\n\n")
+            f.write(f"**Generated:** {datetime.now().isoformat()}\n\n")
+            f.write(f"**Repository:** {stats.get('repository_path', 'Unknown')}\n\n")
+            
+            # Summary statistics
+            f.write("## Summary Statistics\n\n")
+            f.write(f"- **Total Files:** {stats.get('total_files', 0)}\n")
+            f.write(f"- **Total Contributors:** {stats.get('total_contributors', 0)}\n\n")
+            
+            # Categories
+            if 'categories' in stats:
+                f.write("### Files by Category\n\n")
+                for category, count in sorted(stats['categories'].items()):
+                    f.write(f"- **{category}:** {count} files\n")
+                f.write("\n")
+            
+            # Top contributors
+            if 'contributor_file_counts' in stats:
+                f.write("### Top Contributors by Files Modified\n\n")
+                sorted_contributors = sorted(
+                    stats['contributor_file_counts'].items(), 
+                    key=lambda x: x[1], 
+                    reverse=True
+                )[:10]
+                for contributor, count in sorted_contributors:
+                    f.write(f"- **{contributor}:** {count} files\n")
+                f.write("\n")
+            
+            # Detailed file listing
+            f.write("## Detailed File Inventory\n\n")
+            f.write("| File Path | Category | Size (bytes) | Primary Author | Contributors |\n")
+            f.write("|-----------|----------|--------------|----------------|-------------|\n")
+            
+            for entry in sorted(self.inventory, key=lambda x: x['file_path']):
+                contributors_str = ', '.join(entry['contributors'].keys())[:50]
+                if len(contributors_str) == 50:
+                    contributors_str += "..."
+                
+                f.write(f"| {entry['file_path']} | {entry['category']} | "
+                       f"{entry['file_size_bytes']} | {entry['primary_author']} | "
+                       f"{contributors_str} |\n")
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Generate legal file inventory for Basic Memory repository"
+    )
+    parser.add_argument(
+        '--output', '-o',
+        default='basic_memory_legal_inventory.csv',
+        help='Output file path (default: basic_memory_legal_inventory.csv)'
+    )
+    parser.add_argument(
+        '--format', '-f',
+        choices=['csv', 'json', 'markdown'],
+        default='csv',
+        help='Output format (default: csv)'
+    )
+    parser.add_argument(
+        '--repo-path', '-r',
+        default='.',
+        help='Path to repository (default: current directory)'
+    )
+    
+    args = parser.parse_args()
+    
+    # Initialize and run the inventory generator
+    generator = FileInventoryGenerator(args.repo_path)
+    generator.scan_repository()
+    
+    # Export in requested format
+    if args.format == 'csv':
+        generator.export_csv(args.output)
+    elif args.format == 'json':
+        generator.export_json(args.output)
+    elif args.format == 'markdown':
+        generator.export_markdown(args.output)
+    
+    # Print summary
+    stats = generator.get_summary_statistics()
+    print("\n=== Legal File Inventory Complete ===")
+    print(f"Repository: {stats.get('repository_path', 'Unknown')}")
+    print(f"Total files inventoried: {stats.get('total_files', 0)}")
+    print(f"Total contributors identified: {stats.get('total_contributors', 0)}")
+    print(f"Output written to: {args.output}")
+    
+    # Show top contributors
+    if 'contributor_file_counts' in stats:
+        print("\nTop 5 contributors by files modified:")
+        sorted_contributors = sorted(
+            stats['contributor_file_counts'].items(),
+            key=lambda x: x[1],
+            reverse=True
+        )[:5]
+        for i, (contributor, count) in enumerate(sorted_contributors, 1):
+            print(f"  {i}. {contributor}: {count} files")
+
+if __name__ == '__main__':
+    main()

legal_inventory/basic_memory_inventory_20250730_110133.csv

@@ -0,0 +1,272 @@
+path,name,category,size_bytes,modified_time,primary_author,contributor_count,contributors_list,sha256_hash
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legal_inventory_sample.md

@@ -0,0 +1,294 @@
+# Basic Memory - Legal File Inventory
+
+**Generated:** 2025-07-29T16:10:54.745774
+
+**Repository:** /Users/phernandez/dev/basicmachines/basic-memory
+
+## Summary Statistics
+
+- **Total Files:** 255
+- **Total Contributors:** 12
+
+### Files by Category
+
+- **Build/Deployment:** 2 files
+- **Configuration:** 6 files
+- **Database/Migration:** 1 files
+- **Documentation:** 6 files
+- **Legal/License:** 3 files
+- **Other:** 13 files
+- **Source Code:** 222 files
+- **Templates/Resources:** 2 files
+
+### Top Contributors by Files Modified
+
+- **phernandez:** 190 files
+- **Paul Hernandez:** 181 files
+- **bm-claudeai:** 135 files
+- **Drew Cain:** 24 files
+- **github-actions[bot]:** 20 files
+- **Amadeusz Wieczorek:** 2 files
+- **semantic-release:** 1 files
+- **Jason Noble:** 1 files
+- **Marc Baiza:** 1 files
+- **Matias Forbord:** 1 files
+
+## Detailed File Inventory
+
+| File Path | Category | Size (bytes) | Primary Author | Contributors |
+|-----------|----------|--------------|----------------|-------------|
+| .claude/commands/release/beta.md | Other | 3103 | phernandez | phernandez |
+| .claude/commands/release/changelog.md | Documentation | 4648 | phernandez | phernandez |
+| .claude/commands/release/release-check.md | Other | 3344 | phernandez | phernandez |
+| .claude/commands/release/release.md | Other | 2925 | phernandez | phernandez |
+| .claude/commands/test-live.md | Other | 18720 | phernandez | phernandez |
+| .claude/settings.local.json | Configuration | 3122 | Unknown |  |
+| .dockerignore | Other | 623 | Paul Hernandez | Paul Hernandez |
+| .python-version | Other | 5 | phernandez | phernandez |
+| CHANGELOG.md | Documentation | 53647 | semantic-release | semantic-release, phernandez |
+| CITATION.cff | Legal/License | 302 | phernandez | phernandez |
+| CLA.md | Legal/License | 1342 | phernandez | phernandez |
+| CLAUDE.md | Other | 12310 | Paul Hernandez | Paul Hernandez, phernandez, Ikko Eltociear Ashimin... |
+| CODE_OF_CONDUCT.md | Other | 509 | phernandez | phernandez |
+| CONTRIBUTING.md | Documentation | 7241 | phernandez | phernandez, Paul Hernandez |
+| Dockerfile | Build/Deployment | 856 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| LICENSE | Legal/License | 34523 | Paul Hernandez | Paul Hernandez |
+| README.md | Documentation | 16261 | phernandez | phernandez, bm-claudeai, Paul Hernandez, Jason Nob... |
+| SECURITY.md | Other | 303 | Paul Hernandez | Paul Hernandez |
+| docker-compose.yml | Configuration | 2534 | Paul Hernandez | Paul Hernandez, phernandez |
+| docs/AI Assistant Guide.md | Documentation | 16423 | Paul Hernandez | Paul Hernandez, phernandez |
+| docs/Docker.md | Documentation | 9088 | Paul Hernandez | Paul Hernandez, phernandez |
+| justfile | Build/Deployment | 5371 | phernandez | phernandez, Drew Cain |
+| legal_file_inventory.py | Source Code | 17407 | Unknown |  |
+| llms-install.md | Other | 2307 | phernandez | phernandez |
+| memory.json | Configuration | 90075 | phernandez | phernandez |
+| pyproject.toml | Configuration | 3279 | phernandez | phernandez, Paul Hernandez, bm-claudeai, Drew Cain... |
+| smithery.yaml | Configuration | 433 | bm-claudeai | bm-claudeai |
+| src/basic_memory/__init__.py | Source Code | 256 | phernandez | phernandez |
+| src/basic_memory/alembic/alembic.ini | Configuration | 3733 | phernandez | phernandez |
+| src/basic_memory/alembic/migrations.py | Source Code | 718 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/alembic/script.py.mako | Database/Migration | 635 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/alembic/versions/3dae7c7b1564_initial_schema.py | Source Code | 4363 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/alembic/versions/502b60eaa905_remove_required_from_entity_permalink.py | Source Code | 1840 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/alembic/versions/5fe1ab1ccebe_add_projects_table.py | Source Code | 4379 | bm-claudeai | bm-claudeai |
+| src/basic_memory/alembic/versions/647e7a75e2cd_project_constraint_fix.py | Source Code | 4210 | phernandez | phernandez |
+| src/basic_memory/alembic/versions/b3c3938bacdb_relation_to_name_unique_index.py | Source Code | 1428 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/alembic/versions/cc7172b46608_update_search_index_schema.py | Source Code | 3679 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/api/__init__.py | Source Code | 72 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/api/app.py | Source Code | 2897 | bm-claudeai | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/api/routers/__init__.py | Source Code | 398 | phernandez | phernandez, bm-claudeai |
+| src/basic_memory/api/routers/directory_router.py | Source Code | 2054 | Paul Hernandez | bm-claudeai, Paul Hernandez |
+| src/basic_memory/api/routers/importer_router.py | Source Code | 4513 | bm-claudeai | bm-claudeai |
+| src/basic_memory/api/routers/knowledge_router.py | Source Code | 9738 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/api/routers/management_router.py | Source Code | 2730 | bm-claudeai | bm-claudeai, phernandez |
+| src/basic_memory/api/routers/memory_router.py | Source Code | 3003 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/api/routers/project_router.py | Source Code | 8239 | bm-claudeai | bm-claudeai, phernandez, Paul Hernandez |
+| src/basic_memory/api/routers/prompt_router.py | Source Code | 9948 | bm-claudeai | bm-claudeai, phernandez |
+| src/basic_memory/api/routers/resource_router.py | Source Code | 8058 | Paul Hernandez | phernandez, Paul Hernandez |
+| src/basic_memory/api/routers/search_router.py | Source Code | 1226 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/api/routers/utils.py | Source Code | 5159 | bm-claudeai | bm-claudeai, Drew Cain |
+| src/basic_memory/api/template_loader.py | Source Code | 8607 | bm-claudeai | bm-claudeai |
+| src/basic_memory/cli/__init__.py | Source Code | 33 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/cli/app.py | Source Code | 2268 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/cli/commands/__init__.py | Source Code | 393 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/cli/commands/db.py | Source Code | 1480 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/cli/commands/import_chatgpt.py | Source Code | 2856 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| src/basic_memory/cli/commands/import_claude_conversations.py | Source Code | 2946 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| src/basic_memory/cli/commands/import_claude_projects.py | Source Code | 2891 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| src/basic_memory/cli/commands/import_memory_json.py | Source Code | 2947 | Paul Hernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/cli/commands/mcp.py | Source Code | 2593 | phernandez | bm-claudeai, phernandez, Paul Hernandez |
+| src/basic_memory/cli/commands/project.py | Source Code | 12252 | phernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/cli/commands/status.py | Source Code | 5809 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/cli/commands/sync.py | Source Code | 8213 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/cli/commands/tool.py | Source Code | 9540 | phernandez | Paul Hernandez, phernandez, github-actions[bot] |
+| src/basic_memory/cli/main.py | Source Code | 465 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/config.py | Source Code | 12620 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai, Drew Cain... |
+| src/basic_memory/db.py | Source Code | 7428 | phernandez | phernandez, Paul Hernandez, Drew Cain, bm-claudeai... |
+| src/basic_memory/deps.py | Source Code | 12144 | bm-claudeai | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/file_utils.py | Source Code | 6700 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/importers/__init__.py | Source Code | 795 | bm-claudeai | bm-claudeai |
+| src/basic_memory/importers/base.py | Source Code | 2531 | bm-claudeai | bm-claudeai |
+| src/basic_memory/importers/chatgpt_importer.py | Source Code | 7372 | bm-claudeai | bm-claudeai |
+| src/basic_memory/importers/claude_conversations_importer.py | Source Code | 5725 | bm-claudeai | bm-claudeai |
+| src/basic_memory/importers/claude_projects_importer.py | Source Code | 5389 | bm-claudeai | bm-claudeai |
+| src/basic_memory/importers/memory_json_importer.py | Source Code | 3986 | bm-claudeai | bm-claudeai, phernandez |
+| src/basic_memory/importers/utils.py | Source Code | 1792 | bm-claudeai | bm-claudeai |
+| src/basic_memory/markdown/__init__.py | Source Code | 501 | phernandez | phernandez |
+| src/basic_memory/markdown/entity_parser.py | Source Code | 4516 | phernandez | phernandez, Paul Hernandez, github-actions[bot] |
+| src/basic_memory/markdown/markdown_processor.py | Source Code | 4968 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/markdown/plugins.py | Source Code | 6639 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/markdown/schemas.py | Source Code | 1896 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/markdown/utils.py | Source Code | 3410 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/mcp/__init__.py | Source Code | 35 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/mcp/async_client.py | Source Code | 925 | Paul Hernandez | phernandez, Paul Hernandez |
+| src/basic_memory/mcp/project_session.py | Source Code | 4203 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/mcp/prompts/__init__.py | Source Code | 615 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/mcp/prompts/ai_assistant_guide.py | Source Code | 821 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/mcp/prompts/continue_conversation.py | Source Code | 1998 | Paul Hernandez | Paul Hernandez, github-actions[bot], bm-claudeai |
+| src/basic_memory/mcp/prompts/recent_activity.py | Source Code | 3311 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/mcp/prompts/search.py | Source Code | 1692 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| src/basic_memory/mcp/prompts/utils.py | Source Code | 5431 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| src/basic_memory/mcp/resources/ai_assistant_guide.md | Other | 14777 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/mcp/resources/project_info.py | Source Code | 1906 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| src/basic_memory/mcp/server.py | Source Code | 1248 | Paul Hernandez | bm-claudeai, phernandez, Paul Hernandez |
+| src/basic_memory/mcp/tools/__init__.py | Source Code | 1619 | Paul Hernandez | phernandez, Paul Hernandez, Drew Cain |
+| src/basic_memory/mcp/tools/auth.py | Source Code | 1231 | phernandez | phernandez |
+| src/basic_memory/mcp/tools/canvas.py | Source Code | 3738 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/mcp/tools/delete_note.py | Source Code | 7346 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/mcp/tools/edit_note.py | Source Code | 13570 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/mcp/tools/list_directory.py | Source Code | 5236 | Paul Hernandez | Paul Hernandez |
+| src/basic_memory/mcp/tools/move_note.py | Source Code | 16708 | phernandez | Paul Hernandez, phernandez |
+| src/basic_memory/mcp/tools/project_management.py | Source Code | 12944 | Paul Hernandez | Paul Hernandez, phernandez, Drew Cain |
+| src/basic_memory/mcp/tools/read_content.py | Source Code | 8596 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| src/basic_memory/mcp/tools/read_note.py | Source Code | 7614 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez, Amadeusz ... |
+| src/basic_memory/mcp/tools/recent_activity.py | Source Code | 4833 | phernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/mcp/tools/search.py | Source Code | 15883 | phernandez | phernandez, github-actions[bot], Paul Hernandez, D... |
+| src/basic_memory/mcp/tools/sync_status.py | Source Code | 10517 | phernandez | phernandez |
+| src/basic_memory/mcp/tools/utils.py | Source Code | 21426 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/mcp/tools/view_note.py | Source Code | 2499 | phernandez | phernandez |
+| src/basic_memory/mcp/tools/write_note.py | Source Code | 6178 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| src/basic_memory/models/__init__.py | Source Code | 333 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/models/base.py | Source Code | 225 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/models/knowledge.py | Source Code | 7087 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/models/project.py | Source Code | 2773 | bm-claudeai | bm-claudeai, phernandez |
+| src/basic_memory/models/search.py | Source Code | 1300 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/repository/__init__.py | Source Code | 327 | Paul Hernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/repository/entity_repository.py | Source Code | 10405 | Drew Cain | phernandez, Paul Hernandez, Drew Cain, bm-claudeai... |
+| src/basic_memory/repository/observation_repository.py | Source Code | 2943 | phernandez | phernandez, bm-claudeai |
+| src/basic_memory/repository/project_info_repository.py | Source Code | 338 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| src/basic_memory/repository/project_repository.py | Source Code | 3159 | bm-claudeai | bm-claudeai |
+| src/basic_memory/repository/relation_repository.py | Source Code | 3179 | phernandez | phernandez, bm-claudeai |
+| src/basic_memory/repository/repository.py | Source Code | 15224 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/repository/search_repository.py | Source Code | 21936 | phernandez | phernandez, Paul Hernandez, github-actions[bot], b... |
+| src/basic_memory/schemas/__init__.py | Source Code | 1674 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/schemas/base.py | Source Code | 6738 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/schemas/delete.py | Source Code | 1180 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/schemas/directory.py | Source Code | 881 | bm-claudeai | bm-claudeai |
+| src/basic_memory/schemas/importer.py | Source Code | 663 | bm-claudeai | bm-claudeai |
+| src/basic_memory/schemas/memory.py | Source Code | 5833 | phernandez | phernandez, Paul Hernandez, Drew Cain, bm-claudeai... |
+| src/basic_memory/schemas/project_info.py | Source Code | 7047 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| src/basic_memory/schemas/prompt.py | Source Code | 3648 | bm-claudeai | bm-claudeai |
+| src/basic_memory/schemas/request.py | Source Code | 3760 | Paul Hernandez | phernandez, Paul Hernandez |
+| src/basic_memory/schemas/response.py | Source Code | 6450 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/schemas/search.py | Source Code | 3657 | phernandez | phernandez, Paul Hernandez, github-actions[bot], b... |
+| src/basic_memory/services/__init__.py | Source Code | 259 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/services/context_service.py | Source Code | 14462 | bm-claudeai | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/services/directory_service.py | Source Code | 6017 | bm-claudeai | bm-claudeai, Paul Hernandez |
+| src/basic_memory/services/entity_service.py | Source Code | 30440 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai, Drew Cain... |
+| src/basic_memory/services/exceptions.py | Source Code | 390 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/services/file_service.py | Source Code | 10059 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/services/initialization.py | Source Code | 6715 | bm-claudeai | Paul Hernandez, bm-claudeai, Drew Cain, phernandez... |
+| src/basic_memory/services/link_resolver.py | Source Code | 4594 | phernandez | phernandez, Paul Hernandez, bm-claudeai, github-ac... |
+| src/basic_memory/services/project_service.py | Source Code | 28386 | bm-claudeai | bm-claudeai, Paul Hernandez, phernandez |
+| src/basic_memory/services/search_service.py | Source Code | 12782 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| src/basic_memory/services/service.py | Source Code | 336 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/services/sync_status_service.py | Source Code | 7504 | phernandez | phernandez, Paul Hernandez |
+| src/basic_memory/sync/__init__.py | Source Code | 156 | Paul Hernandez | Paul Hernandez, phernandez |
+| src/basic_memory/sync/background_sync.py | Source Code | 726 | bm-claudeai | bm-claudeai, phernandez |
+| src/basic_memory/sync/sync_service.py | Source Code | 23387 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai, github-ac... |
+| src/basic_memory/sync/watch_service.py | Source Code | 15316 | Paul Hernandez | phernandez, bm-claudeai, Paul Hernandez |
+| src/basic_memory/templates/prompts/continue_conversation.hbs | Templates/Resources | 3076 | bm-claudeai | bm-claudeai, Drew Cain |
+| src/basic_memory/templates/prompts/search.hbs | Templates/Resources | 3098 | bm-claudeai | bm-claudeai |
+| src/basic_memory/utils.py | Source Code | 7657 | phernandez | phernandez, Paul Hernandez, andyxinweiminicloud, D... |
+| test-int/conftest.py | Source Code | 8203 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_delete_note_integration.py | Source Code | 13175 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_edit_note_integration.py | Source Code | 19822 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_list_directory_integration.py | Source Code | 14744 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_move_note_integration.py | Source Code | 19825 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_project_management_integration.py | Source Code | 33175 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_project_state_sync_integration.py | Source Code | 7728 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_read_content_integration.py | Source Code | 11187 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_read_note_integration.py | Source Code | 1381 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_search_integration.py | Source Code | 14690 | Paul Hernandez | Paul Hernandez, phernandez |
+| test-int/mcp/test_write_note_integration.py | Source Code | 9472 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/Non-MarkdownFileSupport.pdf | Other | 106751 | Unknown |  |
+| tests/Screenshot.png | Other | 190076 | Unknown |  |
+| tests/__init__.py | Source Code | 141 | phernandez | phernandez, Paul Hernandez |
+| tests/api/conftest.py | Source Code | 1404 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| tests/api/test_async_client.py | Source Code | 1382 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/api/test_continue_conversation_template.py | Source Code | 5152 | bm-claudeai | bm-claudeai |
+| tests/api/test_directory_router.py | Source Code | 9376 | Paul Hernandez | bm-claudeai, Paul Hernandez |
+| tests/api/test_importer_router.py | Source Code | 16578 | bm-claudeai | bm-claudeai, Paul Hernandez |
+| tests/api/test_knowledge_router.py | Source Code | 45771 | Paul Hernandez | phernandez, bm-claudeai, Paul Hernandez |
+| tests/api/test_management_router.py | Source Code | 6220 | bm-claudeai | bm-claudeai |
+| tests/api/test_memory_router.py | Source Code | 5555 | phernandez | phernandez, bm-claudeai |
+| tests/api/test_project_router.py | Source Code | 5201 | Paul Hernandez | bm-claudeai, Paul Hernandez, phernandez |
+| tests/api/test_project_router_operations.py | Source Code | 1812 | bm-claudeai | bm-claudeai, Paul Hernandez |
+| tests/api/test_prompt_router.py | Source Code | 5046 | bm-claudeai | bm-claudeai |
+| tests/api/test_resource_router.py | Source Code | 13960 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai |
+| tests/api/test_search_router.py | Source Code | 6409 | phernandez | phernandez, bm-claudeai, Paul Hernandez, github-ac... |
+| tests/api/test_search_template.py | Source Code | 5258 | bm-claudeai | bm-claudeai |
+| tests/api/test_template_loader.py | Source Code | 8035 | bm-claudeai | bm-claudeai |
+| tests/api/test_template_loader_helpers.py | Source Code | 7445 | bm-claudeai | bm-claudeai |
+| tests/cli/conftest.py | Source Code | 1185 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/cli/test_cli_tools.py | Source Code | 13528 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/cli/test_import_chatgpt.py | Source Code | 6719 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/cli/test_import_claude_conversations.py | Source Code | 5028 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/cli/test_import_claude_projects.py | Source Code | 4585 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/cli/test_import_memory_json.py | Source Code | 3532 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/cli/test_project_commands.py | Source Code | 5143 | bm-claudeai | bm-claudeai, Paul Hernandez, phernandez |
+| tests/cli/test_project_info.py | Source Code | 3874 | phernandez | Paul Hernandez, phernandez |
+| tests/cli/test_status.py | Source Code | 4160 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/cli/test_sync.py | Source Code | 3864 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/cli/test_version.py | Source Code | 289 | Paul Hernandez | Paul Hernandez |
+| tests/conftest.py | Source Code | 15286 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| tests/importers/test_importer_base.py | Source Code | 4329 | bm-claudeai | bm-claudeai |
+| tests/importers/test_importer_utils.py | Source Code | 1827 | bm-claudeai | bm-claudeai |
+| tests/markdown/__init__.py | Source Code | 0 | Unknown |  |
+| tests/markdown/test_entity_parser.py | Source Code | 8669 | phernandez | phernandez, Paul Hernandez, github-actions[bot] |
+| tests/markdown/test_markdown_plugins.py | Source Code | 5139 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/markdown/test_markdown_processor.py | Source Code | 5728 | phernandez | phernandez, Paul Hernandez |
+| tests/markdown/test_observation_edge_cases.py | Source Code | 4295 | phernandez | phernandez |
+| tests/markdown/test_parser_edge_cases.py | Source Code | 5142 | phernandez | phernandez |
+| tests/markdown/test_relation_edge_cases.py | Source Code | 3952 | phernandez | phernandez |
+| tests/markdown/test_task_detection.py | Source Code | 401 | Paul Hernandez | Paul Hernandez |
+| tests/mcp/conftest.py | Source Code | 1761 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| tests/mcp/test_prompts.py | Source Code | 5989 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/mcp/test_resource_project_info.py | Source Code | 4885 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/mcp/test_resources.py | Source Code | 549 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/mcp/test_tool_canvas.py | Source Code | 7997 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/mcp/test_tool_delete_note.py | Source Code | 4208 | phernandez | phernandez |
+| tests/mcp/test_tool_edit_note.py | Source Code | 13503 | Paul Hernandez | Paul Hernandez, phernandez, Drew Cain |
+| tests/mcp/test_tool_list_directory.py | Source Code | 7730 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/mcp/test_tool_move_note.py | Source Code | 16346 | Paul Hernandez | Paul Hernandez, phernandez |
+| tests/mcp/test_tool_read_note.py | Source Code | 9741 | Paul Hernandez | Paul Hernandez, phernandez, github-actions[bot], A... |
+| tests/mcp/test_tool_recent_activity.py | Source Code | 3983 | phernandez | phernandez, bm-claudeai |
+| tests/mcp/test_tool_resource.py | Source Code | 6782 | Paul Hernandez | Paul Hernandez, phernandez, github-actions[bot] |
+| tests/mcp/test_tool_search.py | Source Code | 10959 | phernandez | Paul Hernandez, phernandez, github-actions[bot], D... |
+| tests/mcp/test_tool_sync_status.py | Source Code | 6331 | phernandez | phernandez |
+| tests/mcp/test_tool_utils.py | Source Code | 9228 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/mcp/test_tool_view_note.py | Source Code | 10004 | phernandez | phernandez |
+| tests/mcp/test_tool_write_note.py | Source Code | 19537 | Paul Hernandez | phernandez, Paul Hernandez, Drew Cain |
+| tests/repository/test_entity_repository.py | Source Code | 15498 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| tests/repository/test_entity_repository_upsert.py | Source Code | 16983 | Drew Cain | Drew Cain, phernandez |
+| tests/repository/test_observation_repository.py | Source Code | 11786 | phernandez | phernandez, bm-claudeai |
+| tests/repository/test_project_info_repository.py | Source Code | 1186 | bm-claudeai | bm-claudeai |
+| tests/repository/test_project_repository.py | Source Code | 9455 | bm-claudeai | bm-claudeai |
+| tests/repository/test_relation_repository.py | Source Code | 11980 | phernandez | phernandez, bm-claudeai |
+| tests/repository/test_repository.py | Source Code | 5996 | phernandez | phernandez, Paul Hernandez |
+| tests/repository/test_search_repository.py | Source Code | 25471 | bm-claudeai | bm-claudeai, phernandez, Paul Hernandez |
+| tests/schemas/test_memory_url.py | Source Code | 2000 | phernandez | phernandez, Paul Hernandez |
+| tests/schemas/test_memory_url_validation.py | Source Code | 9338 | phernandez | phernandez |
+| tests/schemas/test_schemas.py | Source Code | 16880 | phernandez | phernandez, Paul Hernandez, bm-claudeai, Drew Cain... |
+| tests/schemas/test_search.py | Source Code | 3264 | phernandez | phernandez, Paul Hernandez, github-actions[bot] |
+| tests/services/test_context_service.py | Source Code | 8833 | phernandez | phernandez, bm-claudeai, Paul Hernandez |
+| tests/services/test_directory_service.py | Source Code | 6854 | Paul Hernandez | bm-claudeai, Paul Hernandez |
+| tests/services/test_entity_service.py | Source Code | 59278 | Paul Hernandez | phernandez, Paul Hernandez, bm-claudeai, Drew Cain... |
+| tests/services/test_file_service.py | Source Code | 5243 | phernandez | phernandez |
+| tests/services/test_initialization.py | Source Code | 6939 | bm-claudeai | Paul Hernandez, bm-claudeai, phernandez |
+| tests/services/test_link_resolver.py | Source Code | 13618 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| tests/services/test_project_service.py | Source Code | 23576 | phernandez | bm-claudeai, Paul Hernandez, phernandez |
+| tests/services/test_project_service_operations.py | Source Code | 4679 | bm-claudeai | bm-claudeai, Paul Hernandez |
+| tests/services/test_search_service.py | Source Code | 25299 | Paul Hernandez | phernandez, Paul Hernandez, github-actions[bot] |
+| tests/services/test_sync_status_service.py | Source Code | 9926 | phernandez | phernandez, Paul Hernandez |
+| tests/sync/test_sync_service.py | Source Code | 39659 | phernandez | phernandez, Paul Hernandez, bm-claudeai |
+| tests/sync/test_sync_wikilink_issue.py | Source Code | 1959 | github-actions[bot] | github-actions[bot], Paul Hernandez |
+| tests/sync/test_tmp_files.py | Source Code | 5930 | Paul Hernandez | Paul Hernandez, bm-claudeai, phernandez |
+| tests/sync/test_watch_service.py | Source Code | 14076 | Paul Hernandez | Paul Hernandez, phernandez, bm-claudeai |
+| tests/sync/test_watch_service_edge_cases.py | Source Code | 2169 | Paul Hernandez | Paul Hernandez, bm-claudeai |
+| tests/test_config.py | Source Code | 3680 | Drew Cain | Drew Cain |
+| tests/test_db_migration_deduplication.py | Source Code | 6166 | Paul Hernandez | Paul Hernandez, Drew Cain, phernandez |
+| tests/utils/test_file_utils.py | Source Code | 6199 | phernandez | phernandez, Paul Hernandez |
+| tests/utils/test_parse_tags.py | Source Code | 1691 | github-actions[bot] | github-actions[bot], Paul Hernandez |
+| tests/utils/test_permalink_formatting.py | Source Code | 4193 | phernandez | phernandez, Paul Hernandez |
+| tests/utils/test_utf8_handling.py | Source Code | 5791 | phernandez | phernandez, Paul Hernandez |

scripts/generate_legal_inventory.py

@@ -0,0 +1,483 @@
+#!/usr/bin/env python3
+"""
+Legal File Inventory Generator for Basic Memory
+
+Generates comprehensive file inventory with contributor information
+for legal documentation, copyright assignments, and due diligence.
+
+Usage:
+    python scripts/generate_legal_inventory.py [options]
+
+Output formats:
+    - CSV: Detailed spreadsheet for analysis
+    - JSON: Structured data for integration
+    - Markdown: Human-readable legal report
+"""
+
+import argparse
+import csv
+import hashlib
+import json
+import subprocess
+from collections import defaultdict
+from datetime import datetime
+from pathlib import Path
+from typing import Dict, List
+
+
+class LegalInventoryGenerator:
+    """Generate comprehensive file inventory for legal documentation."""
+    
+    # Files to exclude from legal inventory
+    EXCLUDED_PATTERNS = {
+        # Generated/compiled files
+        '*.pyc', '*.pyo', '*.pyd', '__pycache__',
+        '*.so', '*.dylib', '*.dll',
+        
+        # Build/cache directories
+        'build/', 'dist/', '.eggs/', '*.egg-info/',
+        '.coverage', '.pytest_cache/', '.mypy_cache/',
+        '.ruff_cache/', '.tox/', 'venv/', '.venv/', 'env/', '.env/',
+        'node_modules/', '.npm/', '.yarn/',
+        
+        # IDE and editor files
+        '.vscode/', '.idea/', '*.swp', '*.swo', '*~',
+        '.DS_Store', 'Thumbs.db',
+        
+        # Version control
+        '.git/', '.gitignore',
+        
+        # OS generated
+        'desktop.ini', '*.tmp', '*.temp'
+    }
+    
+    # File categories for legal classification
+    FILE_CATEGORIES = {
+        'source_code': ['.py', '.pyx', '.pyi'],
+        'documentation': ['.md', '.rst', '.txt'],
+        'configuration': ['.toml', '.yaml', '.yml', '.json', '.ini', '.cfg'],
+        'legal': ['LICENSE', 'COPYING', 'COPYRIGHT', '.md'],
+        'build_deployment': ['Dockerfile', 'Makefile', 'justfile', '.sh'],
+        'database': ['.sql', '.sqlite', '.db'],
+        'templates': ['.j2', '.jinja2', '.hbs', '.handlebars'],
+        'data': ['.csv', '.json', '.xml'],
+        'other': []  # Catch-all for uncategorized files
+    }
+    
+    def __init__(self, repo_path: str = "."):
+        """Initialize generator with repository path."""
+        self.repo_path = Path(repo_path).resolve()
+        self.file_inventory: List[Dict] = []
+        self.contributors: Dict[str, Dict] = defaultdict(lambda: {
+            'email': '', 'commits': 0, 'lines_added': 0, 'files': set()
+        })
+        
+    def should_exclude_file(self, file_path: Path) -> bool:
+        """Check if file should be excluded from inventory."""
+        # Check if file is tracked by git (more efficient than check-ignore)
+        try:
+            rel_path = str(file_path.relative_to(self.repo_path))
+            result = subprocess.run([
+                'git', 'ls-files', '--error-unmatch', rel_path
+            ], capture_output=True, cwd=self.repo_path)
+            
+            # If git ls-files returns non-zero, file is not tracked (likely ignored)
+            if result.returncode != 0:
+                return True
+                
+        except Exception:
+            # Fallback to manual exclusion patterns if git fails
+            pass
+        
+        # Additional manual exclusions for safety
+        file_str = str(file_path.relative_to(self.repo_path))
+        
+        for pattern in self.EXCLUDED_PATTERNS:
+            if pattern.endswith('/'):
+                if any(part == pattern[:-1] for part in file_path.parts):
+                    return True
+            elif '*' in pattern:
+                import fnmatch
+                if fnmatch.fnmatch(file_str, pattern):
+                    return True
+            else:
+                if file_path.name == pattern or file_str == pattern:
+                    return True
+        return False
+    
+    def categorize_file(self, file_path: Path) -> str:
+        """Categorize file based on extension and name."""
+        suffix = file_path.suffix.lower()
+        name = file_path.name.upper()
+        
+        # Check legal files by name first
+        if any(legal in name for legal in ['LICENSE', 'COPYING', 'COPYRIGHT', 'CLA']):
+            return 'legal'
+            
+        # Check by extension
+        for category, extensions in self.FILE_CATEGORIES.items():
+            if suffix in extensions:
+                return category
+                
+        return 'other'
+    
+    def get_file_hash(self, file_path: Path) -> str:
+        """Generate SHA-256 hash of file content."""
+        try:
+            with open(file_path, 'rb') as f:
+                return hashlib.sha256(f.read()).hexdigest()
+        except (IOError, OSError):
+            return "ERROR_READING_FILE"
+    
+    def get_git_contributors(self, file_path: Path) -> List[Dict]:
+        """Get contributor information for a specific file."""
+        try:
+            rel_path = file_path.relative_to(self.repo_path)
+            
+            # Get contributors with line counts
+            result = subprocess.run([
+                'git', 'log', '--follow', '--pretty=format:%an|%ae|%ad|%H',
+                '--date=short', '--', str(rel_path)
+            ], capture_output=True, text=True, cwd=self.repo_path)
+            
+            if result.returncode != 0:
+                return []
+                
+            contributors = []
+            seen = set()
+            
+            for line in result.stdout.strip().split('\n'):
+                if not line:
+                    continue
+                    
+                parts = line.split('|')
+                if len(parts) >= 4:
+                    name, email, date, commit_hash = parts[:4]
+                    
+                    # Normalize author names/emails
+                    normalized_name = self.normalize_author_name(name, email)
+                    
+                    if normalized_name not in seen:
+                        contributors.append({
+                            'name': normalized_name,
+                            'email': email,
+                            'first_contribution': date,
+                            'commit_hash': commit_hash
+                        })
+                        seen.add(normalized_name)
+                        
+            return contributors
+            
+        except Exception as e:
+            print(f"Warning: Could not get git info for {file_path}: {e}")
+            return []
+    
+    def normalize_author_name(self, name: str, email: str) -> str:
+        """Normalize author names to handle multiple emails for same person."""
+        # Known mappings for Basic Memory team
+        name_mappings = {
+            'phernandez': 'Paul Hernandez',
+            'Paul Hernandez': 'Paul Hernandez',
+            'drew-cain': 'Drew Cain',
+            'Drew Cain': 'Drew Cain'
+        }
+        
+        # Handle GitHub bot accounts
+        if 'bot' in name.lower() or 'claude' in name.lower():
+            return f"{name} (AI Assistant)"
+            
+        return name_mappings.get(name, name)
+    
+    def get_file_stats(self, file_path: Path) -> Dict:
+        """Get comprehensive file statistics."""
+        try:
+            stat = file_path.stat()
+            rel_path = file_path.relative_to(self.repo_path)
+            
+            # Basic file info
+            file_info = {
+                'path': str(rel_path),
+                'name': file_path.name,
+                'size_bytes': stat.st_size,
+                'modified_time': datetime.fromtimestamp(stat.st_mtime).isoformat(),
+                'category': self.categorize_file(file_path),
+                'sha256_hash': self.get_file_hash(file_path)
+            }
+            
+            # Git information
+            contributors = self.get_git_contributors(file_path)
+            file_info['contributors'] = contributors
+            file_info['primary_author'] = contributors[0]['name'] if contributors else 'Unknown'
+            file_info['contributor_count'] = len(contributors)
+            
+            # Update global contributor stats
+            for contrib in contributors:
+                name = contrib['name']
+                self.contributors[name]['email'] = contrib['email']
+                self.contributors[name]['files'].add(str(rel_path))
+                
+            return file_info
+            
+        except Exception as e:
+            print(f"Error processing {file_path}: {e}")
+            return None
+    
+    def scan_repository(self) -> None:
+        """Scan repository and build file inventory."""
+        print(f"Scanning repository: {self.repo_path}")
+        
+        # Get all git-tracked files first (much more efficient)
+        try:
+            result = subprocess.run([
+                'git', 'ls-files'
+            ], capture_output=True, text=True, cwd=self.repo_path)
+            
+            if result.returncode == 0:
+                tracked_files = [self.repo_path / f for f in result.stdout.strip().split('\n') if f]
+                print(f"Found {len(tracked_files)} git-tracked files")
+                
+                for file_path in tracked_files:
+                    if file_path.is_file():
+                        file_info = self.get_file_stats(file_path)
+                        if file_info:
+                            self.file_inventory.append(file_info)
+            else:
+                print("Warning: Could not get git tracked files, falling back to directory scan")
+                self._fallback_scan()
+                
+        except Exception as e:
+            print(f"Warning: Git command failed ({e}), falling back to directory scan")
+            self._fallback_scan()
+        
+        # Get global git stats
+        self._get_global_git_stats()
+        
+        print(f"Processed {len(self.file_inventory)} files")
+        print(f"Found {len(self.contributors)} contributors")
+    
+    def _fallback_scan(self) -> None:
+        """Fallback directory scan if git commands fail."""
+        for file_path in self.repo_path.rglob('*'):
+            if file_path.is_file() and not self.should_exclude_file(file_path):
+                file_info = self.get_file_stats(file_path)
+                if file_info:
+                    self.file_inventory.append(file_info)
+    
+    def _get_global_git_stats(self) -> None:
+        """Get global contributor statistics from git."""
+        try:
+            # Get commit counts per author
+            result = subprocess.run([
+                'git', 'shortlog', '-sn', '--all'
+            ], capture_output=True, text=True, cwd=self.repo_path)
+            
+            if result.returncode == 0:
+                for line in result.stdout.strip().split('\n'):
+                    if line.strip():
+                        parts = line.strip().split('\t', 1)
+                        if len(parts) == 2:
+                            count, name = parts
+                            normalized_name = self.normalize_author_name(name, '')
+                            self.contributors[normalized_name]['commits'] = int(count)
+                            
+        except Exception as e:
+            print(f"Warning: Could not get global git stats: {e}")
+    
+    def generate_summary(self) -> Dict:
+        """Generate inventory summary statistics."""
+        total_files = len(self.file_inventory)
+        total_size = sum(f['size_bytes'] for f in self.file_inventory)
+        
+        # Category breakdown
+        categories = defaultdict(int)
+        for file_info in self.file_inventory:
+            categories[file_info['category']] += 1
+        
+        # Top contributors
+        top_contributors = sorted(
+            self.contributors.items(),
+            key=lambda x: len(x[1]['files']),
+            reverse=True
+        )[:10]
+        
+        return {
+            'scan_date': datetime.now().isoformat(),
+            'repository_path': str(self.repo_path),
+            'total_files': total_files,
+            'total_size_bytes': total_size,
+            'categories': dict(categories),
+            'contributor_count': len(self.contributors),
+            'top_contributors': [
+                {
+                    'name': name,
+                    'file_count': len(stats['files']),
+                    'commit_count': stats['commits'],
+                    'email': stats['email']
+                }
+                for name, stats in top_contributors
+            ]
+        }
+    
+    def export_csv(self, output_path: str) -> None:
+        """Export inventory to CSV format."""
+        with open(output_path, 'w', newline='', encoding='utf-8') as csvfile:
+            fieldnames = [
+                'path', 'name', 'category', 'size_bytes', 'modified_time',
+                'primary_author', 'contributor_count', 'contributors_list',
+                'sha256_hash'
+            ]
+            
+            writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
+            writer.writeheader()
+            
+            for file_info in sorted(self.file_inventory, key=lambda x: x['path']):
+                contributors_list = '; '.join([
+                    f"{c['name']} ({c['email']})" for c in file_info['contributors']
+                ])
+                
+                writer.writerow({
+                    'path': file_info['path'],
+                    'name': file_info['name'],
+                    'category': file_info['category'],
+                    'size_bytes': file_info['size_bytes'],
+                    'modified_time': file_info['modified_time'],
+                    'primary_author': file_info['primary_author'],
+                    'contributor_count': file_info['contributor_count'],
+                    'contributors_list': contributors_list,
+                    'sha256_hash': file_info['sha256_hash']
+                })
+        
+        print(f"CSV export saved to: {output_path}")
+    
+    def export_json(self, output_path: str) -> None:
+        """Export inventory to JSON format."""
+        # Convert sets to lists for JSON serialization
+        contributors_serializable = {}
+        for name, stats in self.contributors.items():
+            contributors_serializable[name] = {
+                'email': stats['email'],
+                'commits': stats['commits'],
+                'lines_added': stats['lines_added'],
+                'files': list(stats['files'])
+            }
+        
+        data = {
+            'summary': self.generate_summary(),
+            'files': self.file_inventory,
+            'contributors': contributors_serializable
+        }
+        
+        with open(output_path, 'w', encoding='utf-8') as jsonfile:
+            json.dump(data, jsonfile, indent=2, ensure_ascii=False)
+        
+        print(f"JSON export saved to: {output_path}")
+    
+    def export_markdown(self, output_path: str) -> None:
+        """Export inventory to Markdown format for legal documentation."""
+        summary = self.generate_summary()
+        
+        with open(output_path, 'w', encoding='utf-8') as mdfile:
+            mdfile.write("# Basic Memory - Legal File Inventory\n\n")
+            
+            # Summary section
+            mdfile.write("## Summary\n\n")
+            mdfile.write(f"**Scan Date:** {summary['scan_date']}\n")
+            mdfile.write(f"**Repository:** {summary['repository_path']}\n")
+            mdfile.write(f"**Total Files:** {summary['total_files']:,}\n")
+            mdfile.write(f"**Total Size:** {summary['total_size_bytes']:,} bytes\n")
+            mdfile.write(f"**Contributors:** {summary['contributor_count']}\n\n")
+            
+            # Category breakdown
+            mdfile.write("## File Categories\n\n")
+            for category, count in sorted(summary['categories'].items()):
+                mdfile.write(f"- **{category.replace('_', ' ').title()}:** {count} files\n")
+            mdfile.write("\n")
+            
+            # Top contributors
+            mdfile.write("## Contributors\n\n")
+            for contrib in summary['top_contributors']:
+                mdfile.write(f"- **{contrib['name']}** ({contrib['email']}): ")
+                mdfile.write(f"{contrib['file_count']} files, {contrib['commit_count']} commits\n")
+            mdfile.write("\n")
+            
+            # Detailed file listing by category
+            mdfile.write("## Detailed File Inventory\n\n")
+            
+            for category in sorted(summary['categories'].keys()):
+                category_files = [f for f in self.file_inventory if f['category'] == category]
+                if not category_files:
+                    continue
+                    
+                mdfile.write(f"### {category.replace('_', ' ').title()}\n\n")
+                
+                for file_info in sorted(category_files, key=lambda x: x['path']):
+                    mdfile.write(f"**{file_info['path']}**\n")
+                    mdfile.write(f"- Primary Author: {file_info['primary_author']}\n")
+                    mdfile.write(f"- Contributors: {file_info['contributor_count']}\n")
+                    mdfile.write(f"- Size: {file_info['size_bytes']:,} bytes\n")
+                    
+                    if file_info['contributors']:
+                        contributors_str = ', '.join([c['name'] for c in file_info['contributors']])
+                        mdfile.write(f"- All Contributors: {contributors_str}\n")
+                    
+                    mdfile.write(f"- SHA-256: `{file_info['sha256_hash']}`\n\n")
+        
+        print(f"Markdown export saved to: {output_path}")
+
+
+def main():
+    """Main entry point."""
+    parser = argparse.ArgumentParser(
+        description="Generate legal file inventory for Basic Memory repository"
+    )
+    parser.add_argument(
+        '--repo-path', '-r',
+        default='.',
+        help='Path to repository (default: current directory)'
+    )
+    parser.add_argument(
+        '--output-dir', '-o',
+        default='./legal_inventory',
+        help='Output directory for reports (default: ./legal_inventory)'
+    )
+    parser.add_argument(
+        '--formats', '-f',
+        nargs='+',
+        choices=['csv', 'json', 'markdown', 'all'],
+        default=['all'],
+        help='Output formats to generate (default: all)'
+    )
+    
+    args = parser.parse_args()
+    
+    # Create output directory
+    output_dir = Path(args.output_dir)
+    output_dir.mkdir(exist_ok=True)
+    
+    # Generate inventory
+    generator = LegalInventoryGenerator(args.repo_path)
+    generator.scan_repository()
+    
+    # Determine formats to export
+    formats = args.formats
+    if 'all' in formats:
+        formats = ['csv', 'json', 'markdown']
+    
+    # Export in requested formats
+    timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
+    
+    if 'csv' in formats:
+        generator.export_csv(output_dir / f'basic_memory_inventory_{timestamp}.csv')
+    
+    if 'json' in formats:
+        generator.export_json(output_dir / f'basic_memory_inventory_{timestamp}.json')
+    
+    if 'markdown' in formats:
+        generator.export_markdown(output_dir / f'basic_memory_inventory_{timestamp}.md')
+    
+    print("\nLegal inventory generation complete!")
+    print(f"Output saved to: {output_dir}")
+
+
+if __name__ == '__main__':
+    main()

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__ = "0.14.3"
+__version__ = "0.14.4"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

src/basic_memory/alembic/versions/a1b2c3d4e5f6_fix_project_foreign_keys.py

@@ -0,0 +1,53 @@
+"""fix project foreign keys
+
+Revision ID: a1b2c3d4e5f6
+Revises: 647e7a75e2cd
+Create Date: 2025-08-19 22:06:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision: str = "a1b2c3d4e5f6"
+down_revision: Union[str, None] = "647e7a75e2cd"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Re-establish foreign key constraints that were lost during project table recreation.
+    
+    The migration 647e7a75e2cd recreated the project table but did not re-establish
+    the foreign key constraint from entity.project_id to project.id, causing
+    foreign key constraint failures when trying to delete projects with related entities.
+    """
+    # SQLite doesn't allow adding foreign key constraints to existing tables easily
+    # We need to be careful and handle the case where the constraint might already exist
+    
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        # Try to drop existing foreign key constraint (may not exist)
+        try:
+            batch_op.drop_constraint("fk_entity_project_id", type_="foreignkey")
+        except Exception:
+            # Constraint may not exist, which is fine - we'll create it next
+            pass
+        
+        # Add the foreign key constraint with CASCADE DELETE
+        # This ensures that when a project is deleted, all related entities are also deleted
+        batch_op.create_foreign_key(
+            "fk_entity_project_id", 
+            "project", 
+            ["project_id"], 
+            ["id"],
+            ondelete="CASCADE"
+        )
+
+
+def downgrade() -> None:
+    """Remove the foreign key constraint."""
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        batch_op.drop_constraint("fk_entity_project_id", type_="foreignkey")

src/basic_memory/api/routers/resource_router.py

@@ -188,7 +188,7 @@ async def write_resource(
                     "content_type": content_type,
                     "file_path": file_path,
                     "checksum": checksum,
-                    "updated_at": datetime.fromtimestamp(file_stats.st_mtime),
+                    "updated_at": datetime.fromtimestamp(file_stats.st_mtime).astimezone(),
                 },
             )
             status_code = 200
@@ -200,8 +200,8 @@ async def write_resource(
                 content_type=content_type,
                 file_path=file_path,
                 checksum=checksum,
-                created_at=datetime.fromtimestamp(file_stats.st_ctime),
-                updated_at=datetime.fromtimestamp(file_stats.st_mtime),
+                created_at=datetime.fromtimestamp(file_stats.st_ctime).astimezone(),
+                updated_at=datetime.fromtimestamp(file_stats.st_mtime).astimezone(),
             )
             entity = await entity_repository.add(entity)
             status_code = 201

src/basic_memory/cli/commands/project.py

@@ -23,8 +23,8 @@ 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.mcp.tools.utils import call_patch
 from basic_memory.utils import generate_permalink
+from basic_memory.mcp.tools.utils import call_patch
 
 console = Console()
 
@@ -74,7 +74,7 @@ def add_project(
 ) -> None:
     """Add a new project."""
     # Resolve to absolute path
-    resolved_path = os.path.abspath(os.path.expanduser(path))
+    resolved_path = Path(os.path.abspath(os.path.expanduser(path))).as_posix()
 
     try:
         data = {"name": name, "path": resolved_path, "set_default": set_default}
@@ -100,8 +100,8 @@ def remove_project(
 ) -> None:
     """Remove a project from configuration."""
     try:
-        project_name = generate_permalink(name)
-        response = asyncio.run(call_delete(client, f"/projects/{project_name}"))
+        project_permalink = generate_permalink(name)
+        response = asyncio.run(call_delete(client, f"/projects/{project_permalink}"))
         result = ProjectStatusResponse.model_validate(response.json())
 
         console.print(f"[green]{result.message}[/green]")
@@ -119,9 +119,8 @@ def set_default_project(
 ) -> None:
     """Set the default project and activate it for the current session."""
     try:
-        project_name = generate_permalink(name)
-
-        response = asyncio.run(call_put(client, f"/projects/{project_name}/default"))
+        project_permalink = generate_permalink(name)
+        response = asyncio.run(call_put(client, f"/projects/{project_permalink}/default"))
         result = ProjectStatusResponse.model_validate(response.json())
 
         console.print(f"[green]{result.message}[/green]")
@@ -156,15 +155,15 @@ def move_project(
 ) -> None:
     """Move a project to a new location."""
     # Resolve to absolute path
-    resolved_path = os.path.abspath(os.path.expanduser(new_path))
+    resolved_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
 
     try:
         data = {"path": resolved_path}
-        project_name = generate_permalink(name)
 
+        project_permalink = generate_permalink(name)
         current_project = session.get_current_project()
         response = asyncio.run(
-            call_patch(client, f"/{current_project}/project/{project_name}", json=data)
+            call_patch(client, f"/{current_project}/project/{project_permalink}", json=data)
         )
         result = ProjectStatusResponse.model_validate(response.json())
 

src/basic_memory/config.py

@@ -46,7 +46,7 @@ class BasicMemoryConfig(BaseSettings):
 
     projects: Dict[str, str] = Field(
         default_factory=lambda: {
-            "main": str(Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")))
+            "main": Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")).as_posix()
         },
         description="Mapping of project names to their filesystem paths",
     )
@@ -74,6 +74,11 @@ class BasicMemoryConfig(BaseSettings):
         description="Whether to sync changes in real time. default (True)",
     )
 
+    kebab_filenames: bool = Field(
+        default=False,
+        description="Format for generated filenames. False preserves spaces and special chars, True converts them to hyphens for consistency with permalinks",
+    )
+
     # API connection configuration
     api_url: Optional[str] = Field(
         default=None,
@@ -100,9 +105,9 @@ class BasicMemoryConfig(BaseSettings):
         """Ensure configuration is valid after initialization."""
         # Ensure main project exists
         if "main" not in self.projects:  # pragma: no cover
-            self.projects["main"] = str(
+            self.projects["main"] = (
                 Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory"))
-            )
+            ).as_posix()
 
         # Ensure default project is valid
         if self.default_project not in self.projects:  # pragma: no cover
@@ -215,7 +220,7 @@ class ConfigManager:
 
         # Load config, modify it, and save it
         config = self.load_config()
-        config.projects[name] = str(project_path)
+        config.projects[name] = project_path.as_posix()
         self.save_config(config)
         return ProjectConfig(name=name, home=project_path)
 
@@ -242,7 +247,7 @@ class ConfigManager:
 
         # Load config, modify, and save
         config = self.load_config()
-        config.default_project = name
+        config.default_project = project_name
         self.save_config(config)
 
     def get_project(self, name: str) -> Tuple[str, str] | Tuple[None, None]:
@@ -351,15 +356,22 @@ def setup_basic_memory_logging():  # pragma: no cover
         # print("Skipping duplicate logging setup")
         return
 
-    # Check for console logging environment variable
-    console_logging = os.getenv("BASIC_MEMORY_CONSOLE_LOGGING", "false").lower() == "true"
+    # Check for console logging environment variable - accept more truthy values
+    console_logging_env = os.getenv("BASIC_MEMORY_CONSOLE_LOGGING", "false").lower()
+    console_logging = console_logging_env in ("true", "1", "yes", "on")
+
+    # Check for log level environment variable first, fall back to config
+    log_level = os.getenv("BASIC_MEMORY_LOG_LEVEL")
+    if not log_level:
+        config_manager = ConfigManager()
+        log_level = config_manager.config.log_level
 
     config_manager = ConfigManager()
     config = get_project_config()
     setup_logging(
         env=config_manager.config.env,
         home_dir=user_home,  # Use user home for logs
-        log_level=config_manager.config.log_level,
+        log_level=log_level,
         log_file=f"{DATA_DIR_NAME}/basic-memory-{process_name}.log",
         console=console_logging,
     )

src/basic_memory/file_utils.py

@@ -2,9 +2,11 @@
 
 import hashlib
 from pathlib import Path
+import re
 from typing import Any, Dict, Union
 
 import yaml
+import frontmatter
 from loguru import logger
 
 from basic_memory.utils import FilePath
@@ -233,3 +235,66 @@ async def update_frontmatter(path: FilePath, updates: Dict[str, Any]) -> str:
             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:
+    
+    Good (Obsidian compatible):
+    ---
+    tags:
+    - system
+    - overview  
+    - reference
+    ---
+    
+    Bad (current behavior):
+    ---
+    tags: ["system", "overview", "reference"]
+    ---
+    
+    Args:
+        post: frontmatter.Post object to serialize
+        
+    Returns:
+        String containing markdown with properly formatted YAML frontmatter
+    """    
+    if not post.metadata:
+        # No frontmatter, just return content
+        return post.content
+        
+    # Serialize YAML with block style for lists
+    yaml_str = yaml.dump(
+        post.metadata,
+        sort_keys=False,
+        allow_unicode=True,
+        default_flow_style=False
+    )
+    
+    # Construct the final markdown with frontmatter
+    if post.content:
+        return f"---\n{yaml_str}---\n\n{post.content}"
+    else:
+        return f"---\n{yaml_str}---\n"
+
+
+def sanitize_for_filename(text: str, replacement: str = "-") -> str:
+    """
+    Sanitize string to be safe for use as a note title
+    Replaces path separators and other problematic characters
+    with hyphens.
+    """
+    # replace both POSIX and Windows path separators
+    text = re.sub(r"[/\\]", replacement, text)
+
+    # replace some other problematic chars
+    text = re.sub(r'[<>:"|?*]', replacement, text)
+
+    # compress multiple, repeated replacements
+    text = re.sub(f"{re.escape(replacement)}+", replacement, text)
+
+    return text.strip(replacement)
+

src/basic_memory/importers/chatgpt_importer.py

@@ -93,7 +93,7 @@ class ChatGPTImporter(Importer[ChatImportResult]):
                 break
 
         # Generate permalink
-        date_prefix = datetime.fromtimestamp(created_at).strftime("%Y%m%d")
+        date_prefix = datetime.fromtimestamp(created_at).astimezone().strftime("%Y%m%d")
         clean_title = clean_filename(conversation["title"])
 
         # Format content

src/basic_memory/importers/utils.py

@@ -43,13 +43,13 @@ def format_timestamp(timestamp: Any) -> str:  # pragma: no cover
         except ValueError:
             try:
                 # Try unix timestamp as string
-                timestamp = datetime.fromtimestamp(float(timestamp))
+                timestamp = datetime.fromtimestamp(float(timestamp)).astimezone()
             except ValueError:
                 # Return as is if we can't parse it
                 return timestamp
     elif isinstance(timestamp, (int, float)):
         # Unix timestamp
-        timestamp = datetime.fromtimestamp(timestamp)
+        timestamp = datetime.fromtimestamp(timestamp).astimezone()
 
     if isinstance(timestamp, datetime):
         return timestamp.strftime("%Y-%m-%d %H:%M:%S")

src/basic_memory/markdown/entity_parser.py

@@ -130,6 +130,6 @@ class EntityParser:
             content=post.content,
             observations=entity_content.observations,
             relations=entity_content.relations,
-            created=datetime.fromtimestamp(file_stats.st_ctime),
-            modified=datetime.fromtimestamp(file_stats.st_mtime),
+            created=datetime.fromtimestamp(file_stats.st_ctime).astimezone(),
+            modified=datetime.fromtimestamp(file_stats.st_mtime).astimezone(),
         )

src/basic_memory/markdown/markdown_processor.py

@@ -2,11 +2,11 @@ from pathlib import Path
 from typing import Optional
 from collections import OrderedDict
 
-import frontmatter
 from frontmatter import Post
 from loguru import logger
 
 from basic_memory import file_utils
+from basic_memory.file_utils import dump_frontmatter
 from basic_memory.markdown.entity_parser import EntityParser
 from basic_memory.markdown.schemas import EntityMarkdown, Observation, Relation
 
@@ -115,7 +115,7 @@ class MarkdownProcessor:
 
         # Create Post object for frontmatter
         post = Post(content, **frontmatter_dict)
-        final_content = frontmatter.dumps(post, sort_keys=False)
+        final_content = dump_frontmatter(post)
 
         logger.debug(f"writing file {path} with content:\n{final_content}")
 

src/basic_memory/markdown/plugins.py

@@ -8,35 +8,49 @@ from markdown_it.token import Token
 # Observation handling functions
 def is_observation(token: Token) -> bool:
     """Check if token looks like our observation format."""
+    import re
     if token.type != "inline":  # pragma: no cover
         return False
-
-    content = token.content.strip()
+    # Use token.tag which contains the actual content for test tokens, fallback to content
+    content = (token.tag or token.content).strip()
     if not content:  # pragma: no cover
         return False
-
     # if it's a markdown_task, return false
     if content.startswith("[ ]") or content.startswith("[x]") or content.startswith("[-]"):
         return False
-
-    has_category = content.startswith("[") and "]" in content
+    
+    # Exclude markdown links: [text](url)
+    if re.match(r"^\[.*?\]\(.*?\)$", content):
+        return False
+    
+    # Exclude wiki links: [[text]]
+    if re.match(r"^\[\[.*?\]\]$", content):
+        return False
+    
+    # Check for proper observation format: [category] content
+    match = re.match(r"^\[([^\[\]()]+)\]\s+(.+)", content)
     has_tags = "#" in content
-    return has_category or has_tags
+    return bool(match) or has_tags
 
 
 def parse_observation(token: Token) -> Dict[str, Any]:
     """Extract observation parts from token."""
-    # Strip bullet point if present
-    content = token.content.strip()
-
-    # Parse [category]
+    import re
+    # Use token.tag which contains the actual content for test tokens, fallback to content
+    content = (token.tag or token.content).strip()
+    
+    # Parse [category] with regex
+    match = re.match(r"^\[([^\[\]()]+)\]\s+(.+)", content)
     category = None
-    if content.startswith("["):
-        end = content.find("]")
-        if end != -1:
-            category = content[1:end].strip() or None  # Convert empty to None
-            content = content[end + 1 :].strip()
-
+    if match:
+        category = match.group(1).strip()
+        content = match.group(2).strip()
+    else:
+        # Handle empty brackets [] followed by content
+        empty_match = re.match(r"^\[\]\s+(.+)", content)
+        if empty_match:
+            content = empty_match.group(1).strip()
+    
     # Parse (context)
     context = None
     if content.endswith(")"):
@@ -44,20 +58,18 @@ def parse_observation(token: Token) -> Dict[str, Any]:
         if start != -1:
             context = content[start + 1 : -1].strip()
             content = content[:start].strip()
-
+    
     # Extract tags and keep original content
     tags = []
     parts = content.split()
     for part in parts:
         if part.startswith("#"):
-            # Handle multiple #tags stuck together
             if "#" in part[1:]:
-                # Split on # but keep non-empty tags
                 subtags = [t for t in part.split("#") if t]
                 tags.extend(subtags)
             else:
                 tags.append(part[1:])
-
+    
     return {
         "category": category,
         "content": content,
@@ -72,14 +84,16 @@ def is_explicit_relation(token: Token) -> bool:
     if token.type != "inline":  # pragma: no cover
         return False
 
-    content = token.content.strip()
+    # Use token.tag which contains the actual content for test tokens, fallback to content
+    content = (token.tag or token.content).strip()
     return "[[" in content and "]]" in content
 
 
 def parse_relation(token: Token) -> Dict[str, Any] | None:
     """Extract relation parts from token."""
     # Remove bullet point if present
-    content = token.content.strip()
+    # Use token.tag which contains the actual content for test tokens, fallback to content
+    content = (token.tag or token.content).strip()
 
     # Extract [[target]]
     target = None
@@ -213,10 +227,12 @@ def relation_plugin(md: MarkdownIt) -> None:
                         token.meta["relations"] = [rel]
 
                 # Always check for inline links in any text
-                elif "[[" in token.content:
-                    rels = parse_inline_relations(token.content)
-                    if rels:
-                        token.meta["relations"] = token.meta.get("relations", []) + rels
+                else:
+                    content = token.tag or token.content
+                    if "[[" in content:
+                        rels = parse_inline_relations(content)
+                        if rels:
+                            token.meta["relations"] = token.meta.get("relations", []) + rels
 
     # Add the rule after inline processing
     md.core.ruler.after("inline", "relations", relation_rule)

src/basic_memory/markdown/utils.py

@@ -41,7 +41,7 @@ def entity_model_from_markdown(
     # Only update permalink if it exists in frontmatter, otherwise preserve existing
     if markdown.frontmatter.permalink is not None:
         model.permalink = markdown.frontmatter.permalink
-    model.file_path = str(file_path)
+    model.file_path = file_path.as_posix()
     model.content_type = "text/markdown"
     model.created_at = markdown.created
     model.updated_at = markdown.modified

src/basic_memory/mcp/tools/build_context.py

@@ -15,6 +15,7 @@ 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.
@@ -35,7 +36,7 @@ from basic_memory.schemas.memory import (
 )
 async def build_context(
     url: MemoryUrl,
-    depth: Optional[int] = 1,
+    depth: Optional[StringOrInt] = 1,
     timeframe: Optional[TimeFrame] = "7d",
     page: int = 1,
     page_size: int = 10,
@@ -80,6 +81,15 @@ async def build_context(
         build_context("memory://specs/search", project="work-project")
     """
     logger.info(f"Building context from {url}")
+    
+    # Convert string depth to integer if needed
+    if isinstance(depth, str):
+        try:
+            depth = int(depth)
+        except ValueError:
+            from mcp.server.fastmcp.exceptions import ToolError
+            raise ToolError(f"Invalid depth parameter: '{depth}' is not a valid integer")
+    
     # URL is already validated and normalized by MemoryUrl type annotation
 
     # Get the active project first to check project-specific sync status
@@ -101,7 +111,7 @@ async def build_context(
             metadata=MemoryMetadata(
                 depth=depth or 1,
                 timeframe=timeframe,
-                generated_at=datetime.now(),
+                generated_at=datetime.now().astimezone(),
                 primary_count=0,
                 related_count=0,
                 uri=migration_status,  # Include status in metadata

src/basic_memory/mcp/tools/project_management.py

@@ -221,8 +221,10 @@ async def set_default_project(project_name: str, ctx: Context | None = None) ->
     if ctx:  # pragma: no cover
         await ctx.info(f"Setting default project to: {project_name}")
 
-    # Call API to set default project
-    response = await call_put(client, f"/projects/{project_name}/default")
+    # Call API to set default project using URL encoding for special characters
+    from urllib.parse import quote
+    encoded_name = quote(project_name, safe='')
+    response = await call_put(client, f"/projects/{encoded_name}/default")
     status_response = ProjectStatusResponse.model_validate(response.json())
 
     result = f"✓ {status_response.message}\n\n"
@@ -323,16 +325,29 @@ async def delete_project(project_name: str, ctx: Context | None = None) -> str:
     response = await call_get(client, "/projects/projects")
     project_list = ProjectList.model_validate(response.json())
 
-    # Check if project exists
-    project_exists = any(p.name == project_name for p in project_list.projects)
-    if not project_exists:
+    # Find the project by name (case-insensitive) or permalink - same logic as switch_project
+    project_permalink = generate_permalink(project_name)
+    target_project = None
+    for p in project_list.projects:
+        # Match by permalink (handles case-insensitive input)
+        if p.permalink == project_permalink:
+            target_project = p
+            break
+        # Also match by name comparison (case-insensitive)
+        if p.name.lower() == project_name.lower():
+            target_project = p
+            break
+    
+    if not target_project:
         available_projects = [p.name for p in project_list.projects]
         raise ValueError(
             f"Project '{project_name}' not found. Available projects: {', '.join(available_projects)}"
         )
 
-    # Call API to delete project
-    response = await call_delete(client, f"/projects/{project_name}")
+    # Call API to delete project using URL encoding for special characters
+    from urllib.parse import quote
+    encoded_name = quote(target_project.name, safe='')
+    response = await call_delete(client, f"/projects/{encoded_name}")
     status_response = ProjectStatusResponse.model_validate(response.json())
 
     result = f"✓ {status_response.message}\n\n"

src/basic_memory/mcp/tools/read_note.py

@@ -56,6 +56,20 @@ async def read_note(
     # Get the active project first to check project-specific sync status
     active_project = get_active_project(project)
 
+    # Validate identifier to prevent path traversal attacks
+    # We need to check both the raw identifier and the processed path
+    processed_path = memory_url_path(identifier)
+    project_path = active_project.home
+    
+    if not validate_project_path(identifier, project_path) or not validate_project_path(processed_path, project_path):
+        logger.warning(
+            "Attempted path traversal attack blocked",
+            identifier=identifier,
+            processed_path=processed_path,
+            project=active_project.name,
+        )
+        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
 
@@ -68,17 +82,6 @@ async def read_note(
 
     # Get the file via REST API - first try direct permalink lookup
     entity_path = memory_url_path(identifier)
-
-    # Validate path to prevent path traversal attacks
-    project_path = active_project.home
-    if not validate_project_path(entity_path, project_path):
-        logger.warning(
-            "Attempted path traversal attack blocked",
-            identifier=identifier,
-            entity_path=entity_path,
-            project=active_project.name,
-        )
-        return f"# Error\n\nPath '{identifier}' is not allowed - paths must stay within project boundaries"
     path = f"{project_url}/resource/{entity_path}"
     logger.info(f"Attempting to read note from URL: {path}")
 
@@ -136,7 +139,7 @@ def format_not_found_message(identifier: str) -> str:
     return dedent(f"""
         # Note Not Found: "{identifier}"
         
-        I searched for "{identifier}" using multiple methods (direct lookup, title search, and text search) but couldn't find any matching notes. Here are some suggestions:
+        I couldn't find any notes matching "{identifier}". Here are some suggestions:
         
         ## Check Identifier Type
         - If you provided a title, try using the exact permalink instead
@@ -182,7 +185,7 @@ def format_related_results(identifier: str, results) -> str:
     message = dedent(f"""
         # Note Not Found: "{identifier}"
         
-        I searched for "{identifier}" using direct lookup and title search but couldn't find an exact match. However, I found some related notes through text search:
+        I couldn't find an exact match for "{identifier}", but I found some related notes:
         
         """)
 

src/basic_memory/models/knowledge.py

@@ -1,6 +1,7 @@
 """Knowledge graph models."""
 
 from datetime import datetime
+from basic_memory.utils import ensure_timezone_aware
 from typing import Optional
 
 from sqlalchemy import (
@@ -73,8 +74,8 @@ class Entity(Base):
     checksum: Mapped[Optional[str]] = mapped_column(String, nullable=True)
 
     # Metadata and tracking
-    created_at: Mapped[datetime] = mapped_column(DateTime)
-    updated_at: Mapped[datetime] = mapped_column(DateTime)
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now().astimezone())
+    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now().astimezone(), onupdate=lambda: datetime.now().astimezone())
 
     # Relationships
     project = relationship("Project", back_populates="entities")
@@ -103,6 +104,16 @@ class Entity(Base):
     def is_markdown(self):
         """Check if the entity is a markdown file."""
         return self.content_type == "text/markdown"
+    
+    def __getattribute__(self, name):
+        """Override attribute access to ensure datetime fields are timezone-aware."""
+        value = super().__getattribute__(name)
+        
+        # Ensure datetime fields are timezone-aware
+        if name in ('created_at', 'updated_at') and isinstance(value, datetime):
+            return ensure_timezone_aware(value)
+        
+        return value
 
     def __repr__(self) -> str:
         return f"Entity(id={self.id}, name='{self.title}', type='{self.entity_type}'"

src/basic_memory/models/project.py

@@ -52,9 +52,9 @@ class Project(Base):
     is_default: Mapped[Optional[bool]] = mapped_column(Boolean, default=None, nullable=True)
 
     # Timestamps
-    created_at: Mapped[datetime] = mapped_column(DateTime, default=lambda: datetime.now(UTC))
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
     updated_at: Mapped[datetime] = mapped_column(
-        DateTime, default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC)
+        DateTime(timezone=True), default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC)
     )
 
     # Define relationships to entities, observations, and relations

src/basic_memory/repository/entity_repository.py

@@ -57,7 +57,7 @@ class EntityRepository(Repository[Entity]):
         """
         query = (
             self.select()
-            .where(Entity.file_path == str(file_path))
+            .where(Entity.file_path == Path(file_path).as_posix())
             .options(*self.get_load_options())
         )
         return await self.find_one(query)
@@ -68,7 +68,7 @@ class EntityRepository(Repository[Entity]):
         Args:
             file_path: Path to the entity file (will be converted to string internally)
         """
-        return await self.delete_by_fields(file_path=str(file_path))
+        return await self.delete_by_fields(file_path=Path(file_path).as_posix())
 
     def get_load_options(self) -> List[LoaderOption]:
         """Get SQLAlchemy loader options for eager loading relationships."""

src/basic_memory/repository/project_repository.py

@@ -46,7 +46,7 @@ class ProjectRepository(Repository[Project]):
         Args:
             path: Path to the project directory (will be converted to string internally)
         """
-        query = self.select().where(Project.path == str(path))
+        query = self.select().where(Project.path == Path(path).as_posix())
         return await self.find_one(query)
 
     async def get_default_project(self) -> Optional[Project]:

src/basic_memory/repository/search_repository.py

@@ -6,6 +6,7 @@ import time
 from dataclasses import dataclass
 from datetime import datetime
 from typing import Any, Dict, List, Optional
+from pathlib import Path
 
 from loguru import logger
 from sqlalchemy import Executable, Result, text
@@ -59,8 +60,11 @@ class SearchIndexRow:
         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 = self.file_path.split("/")
+        parts = normalized_path.split("/")
 
         # If there's only one part (e.g., "README.md"), it's at the root
         if len(parts) <= 1:
@@ -523,8 +527,8 @@ class SearchRepository:
         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"),
-                {"permalink": search_index_row.permalink},
+                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

src/basic_memory/schemas/base.py

@@ -22,6 +22,8 @@ from dateparser import parse
 
 from pydantic import BaseModel, BeforeValidator, Field, model_validator
 
+from basic_memory.config import ConfigManager
+from basic_memory.file_utils import sanitize_for_filename
 from basic_memory.utils import generate_permalink
 
 
@@ -53,22 +55,28 @@ def parse_timeframe(timeframe: str) -> datetime:
         timeframe: Natural language timeframe like 'today', '1d', '1 week ago', etc.
 
     Returns:
-        datetime: The parsed datetime for the start of the timeframe
+        datetime: The parsed datetime for the start of the timeframe, timezone-aware in local system timezone
 
     Examples:
-        parse_timeframe('today') -> 2025-06-05 00:00:00 (start of today)
-        parse_timeframe('1d') -> 2025-06-04 14:50:00 (24 hours ago)
-        parse_timeframe('1 week ago') -> 2025-05-29 14:50:00 (1 week ago)
+        parse_timeframe('today') -> 2025-06-05 00:00:00-07:00 (start of today with local timezone)
+        parse_timeframe('1d') -> 2025-06-04 14:50:00-07:00 (24 hours ago with local timezone)
+        parse_timeframe('1 week ago') -> 2025-05-29 14:50:00-07:00 (1 week ago with local timezone)
     """
     if timeframe.lower() == "today":
-        # Return start of today (00:00:00)
-        return datetime.combine(datetime.now().date(), time.min)
+        # Return start of today (00:00:00) in local timezone
+        naive_dt = datetime.combine(datetime.now().date(), time.min)
+        return naive_dt.astimezone()
     else:
         # Use dateparser for other formats
         parsed = parse(timeframe)
         if not parsed:
             raise ValueError(f"Could not parse timeframe: {timeframe}")
-        return parsed
+        
+        # If the parsed datetime is naive, make it timezone-aware in local system timezone
+        if parsed.tzinfo is None:
+            return parsed.astimezone()
+        else:
+            return parsed
 
 
 def validate_timeframe(timeframe: str) -> str:
@@ -85,7 +93,7 @@ def validate_timeframe(timeframe: str) -> str:
     parsed = parse_timeframe(timeframe)
 
     # Convert to duration
-    now = datetime.now()
+    now = datetime.now().astimezone()
     if parsed > now:
         raise ValueError("Timeframe cannot be in the future")
 
@@ -184,13 +192,35 @@ class Entity(BaseModel):
         default="text/markdown",
     )
 
+    @property
+    def safe_title(self) -> str:
+        """
+        A sanitized version of the title, which is safe for use on the filesystem. For example,
+        a title of "Coupon Enable/Disable Feature" should create a the file as "Coupon Enable-Disable Feature.md"
+        instead of creating a file named "Disable Feature.md" beneath the "Coupon Enable" directory.
+
+        Replaces POSIX and/or Windows style slashes as well as a few other characters that are not safe for filenames.
+        If kebab_filenames is True, then behavior is consistent with transformation used when generating permalink
+        strings (e.g. "Coupon Enable/Disable Feature" -> "coupon-enable-disable-feature").
+        """
+        fixed_title = sanitize_for_filename(self.title)
+
+        app_config = ConfigManager().config
+        use_kebab_case = app_config.kebab_filenames
+
+        if use_kebab_case:
+            fixed_title = generate_permalink(file_path=fixed_title, split_extension=False)
+
+        return fixed_title
+
     @property
     def file_path(self):
         """Get the file path for this entity based on its permalink."""
+        safe_title = self.safe_title
         if self.content_type == "text/markdown":
-            return f"{self.folder}/{self.title}.md" if self.folder else f"{self.title}.md"
+            return f"{self.folder}/{safe_title}.md" if self.folder else f"{safe_title}.md"
         else:
-            return f"{self.folder}/{self.title}" if self.folder else self.title
+            return f"{self.folder}/{safe_title}" if self.folder else safe_title
 
     @property
     def permalink(self) -> Permalink:

src/basic_memory/schemas/memory.py

@@ -1,10 +1,10 @@
 """Schemas for memory context."""
 
 from datetime import datetime
-from typing import List, Optional, Annotated, Sequence
+from typing import List, Optional, Annotated, Sequence, Literal, Union
 
 from annotated_types import MinLen, MaxLen
-from pydantic import BaseModel, Field, BeforeValidator, TypeAdapter
+from pydantic import BaseModel, Field, BeforeValidator, TypeAdapter, ConfigDict
 
 from basic_memory.schemas.search import SearchItemType
 
@@ -117,8 +117,10 @@ def memory_url_path(url: memory_url) -> str:  # pyright: ignore
 
 class EntitySummary(BaseModel):
     """Simplified entity representation."""
+    
+    model_config = ConfigDict(json_encoders={datetime: lambda dt: dt.isoformat()})
 
-    type: str = "entity"
+    type: Literal["entity"] = "entity"
     permalink: Optional[str]
     title: str
     content: Optional[str] = None
@@ -128,8 +130,10 @@ class EntitySummary(BaseModel):
 
 class RelationSummary(BaseModel):
     """Simplified relation representation."""
+    
+    model_config = ConfigDict(json_encoders={datetime: lambda dt: dt.isoformat()})
 
-    type: str = "relation"
+    type: Literal["relation"] = "relation"
     title: str
     file_path: str
     permalink: str
@@ -141,8 +145,10 @@ class RelationSummary(BaseModel):
 
 class ObservationSummary(BaseModel):
     """Simplified observation representation."""
+    
+    model_config = ConfigDict(json_encoders={datetime: lambda dt: dt.isoformat()})
 
-    type: str = "observation"
+    type: Literal["observation"] = "observation"
     title: str
     file_path: str
     permalink: str
@@ -153,6 +159,8 @@ class ObservationSummary(BaseModel):
 
 class MemoryMetadata(BaseModel):
     """Simplified response metadata."""
+    
+    model_config = ConfigDict(json_encoders={datetime: lambda dt: dt.isoformat()})
 
     uri: Optional[str] = None
     types: Optional[List[SearchItemType]] = None
@@ -169,17 +177,21 @@ class MemoryMetadata(BaseModel):
 class ContextResult(BaseModel):
     """Context result containing a primary item with its observations and related items."""
 
-    primary_result: EntitySummary | RelationSummary | ObservationSummary = Field(
-        description="Primary item"
-    )
+    primary_result: Annotated[
+        Union[EntitySummary, RelationSummary, ObservationSummary], 
+        Field(discriminator="type", description="Primary item")
+    ]
 
     observations: Sequence[ObservationSummary] = Field(
         description="Observations belonging to this entity", default_factory=list
     )
 
-    related_results: Sequence[EntitySummary | RelationSummary | ObservationSummary] = Field(
-        description="Related items", default_factory=list
-    )
+    related_results: Sequence[
+        Annotated[
+            Union[EntitySummary, RelationSummary, ObservationSummary], 
+            Field(discriminator="type")
+        ]
+    ] = Field(description="Related items", default_factory=list)
 
 
 class GraphContext(BaseModel):

src/basic_memory/services/context_service.py

@@ -245,8 +245,8 @@ class ContextService:
         # 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
-        params = {"max_depth": max_depth, "max_results": max_results}
+        # Parameters for bindings - include project_id for security filtering
+        params = {"max_depth": max_depth, "max_results": max_results, "project_id": self.search_repository.project_id}
 
         # Build date and timeframe filters conditionally based on since parameter
         if since:
@@ -258,6 +258,10 @@ class ContextService:
             date_filter = ""
             relation_date_filter = ""
             timeframe_condition = ""
+        
+        # Add project filtering for security - ensure all entities and relations belong to the same project
+        project_filter = "AND e.project_id = :project_id"
+        relation_project_filter = "AND e_from.project_id = :project_id"
 
         # Use a CTE that operates directly on entity and relation tables
         # This avoids the overhead of the search_index virtual table
@@ -284,6 +288,7 @@ class ContextService:
             FROM entity e
             WHERE e.id IN ({entity_id_values})
             {date_filter}
+            {project_filter}
 
             UNION ALL
 
@@ -314,8 +319,12 @@ class ContextService:
             JOIN entity e_from ON (
                 r.from_id = e_from.id
                 {relation_date_filter}
+                {relation_project_filter}
             )
+            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
 
@@ -348,6 +357,7 @@ class ContextService:
                     ELSE eg.from_id
                 END
                 {date_filter}
+                {project_filter}
             )
             WHERE eg.depth < :max_depth
             -- Only include entities connected by relations within timeframe if specified

src/basic_memory/services/directory_service.py

@@ -106,8 +106,15 @@ class DirectoryService:
             List of DirectoryNode objects matching the criteria
         """
         # Normalize directory path
+        # Strip ./ prefix if present (handles relative path notation)
+        if dir_name.startswith("./"):
+            dir_name = dir_name[2:]  # Remove "./" prefix
+
+        # Ensure path starts with "/"
         if not dir_name.startswith("/"):
             dir_name = f"/{dir_name}"
+
+        # Remove trailing slashes except for root
         if dir_name != "/" and dir_name.endswith("/"):
             dir_name = dir_name.rstrip("/")
 

src/basic_memory/services/entity_service.py

@@ -9,7 +9,7 @@ from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
 from basic_memory.config import ProjectConfig, BasicMemoryConfig
-from basic_memory.file_utils import has_frontmatter, parse_frontmatter, remove_frontmatter
+from basic_memory.file_utils import has_frontmatter, parse_frontmatter, remove_frontmatter, dump_frontmatter
 from basic_memory.markdown import EntityMarkdown
 from basic_memory.markdown.entity_parser import EntityParser
 from basic_memory.markdown.utils import entity_model_from_markdown, schema_to_markdown
@@ -91,7 +91,7 @@ class EntityService(BaseService[EntityModel]):
 
         Enhanced to detect and handle character-related conflicts.
         """
-        file_path_str = str(file_path)
+        file_path_str = Path(file_path).as_posix()
 
         # Check for potential file path conflicts before resolving permalink
         conflicts = await self.detect_file_path_conflicts(file_path_str)
@@ -119,7 +119,7 @@ class EntityService(BaseService[EntityModel]):
         if markdown and markdown.frontmatter.permalink:
             desired_permalink = markdown.frontmatter.permalink
         else:
-            desired_permalink = generate_permalink(file_path)
+            desired_permalink = generate_permalink(file_path_str)
 
         # Make unique if needed - enhanced to handle character conflicts
         permalink = desired_permalink
@@ -196,7 +196,7 @@ class EntityService(BaseService[EntityModel]):
         post = await schema_to_markdown(schema)
 
         # write file
-        final_content = frontmatter.dumps(post, sort_keys=False)
+        final_content = dump_frontmatter(post)
         checksum = await self.file_service.write_file(file_path, final_content)
 
         # parse entity from file
@@ -273,7 +273,7 @@ class EntityService(BaseService[EntityModel]):
         merged_post = frontmatter.Post(post.content, **existing_markdown.frontmatter.metadata)
 
         # write file
-        final_content = frontmatter.dumps(merged_post, sort_keys=False)
+        final_content = dump_frontmatter(merged_post)
         checksum = await self.file_service.write_file(file_path, final_content)
 
         # parse entity from file
@@ -283,7 +283,7 @@ class EntityService(BaseService[EntityModel]):
         entity = await self.update_entity_and_observations(file_path, entity_markdown)
 
         # add relations
-        await self.update_entity_relations(str(file_path), entity_markdown)
+        await self.update_entity_relations(file_path.as_posix(), entity_markdown)
 
         # Set final checksum to match file
         entity = await self.repository.update(entity.id, {"checksum": checksum})
@@ -374,7 +374,7 @@ class EntityService(BaseService[EntityModel]):
         """
         logger.debug(f"Updating entity and observations: {file_path}")
 
-        db_entity = await self.repository.get_by_file_path(str(file_path))
+        db_entity = await self.repository.get_by_file_path(file_path.as_posix())
 
         # Clear observations for entity
         await self.observation_repository.delete_by_fields(entity_id=db_entity.id)
@@ -498,7 +498,7 @@ class EntityService(BaseService[EntityModel]):
 
         # Update entity and its relationships
         entity = await self.update_entity_and_observations(file_path, entity_markdown)
-        await self.update_entity_relations(str(file_path), entity_markdown)
+        await self.update_entity_relations(file_path.as_posix(), entity_markdown)
 
         # Set final checksum to match file
         entity = await self.repository.update(entity.id, {"checksum": checksum})

src/basic_memory/services/project_service.py

@@ -100,7 +100,7 @@ class ProjectService:
             raise ValueError("Repository is required for add_project")
 
         # Resolve to absolute path
-        resolved_path = os.path.abspath(os.path.expanduser(path))
+        resolved_path = Path(os.path.abspath(os.path.expanduser(path))).as_posix()
 
         # First add to config file (this will validate the project doesn't exist)
         project_config = self.config_manager.add_project(name, resolved_path)
@@ -139,8 +139,8 @@ class ProjectService:
         # First remove from config (this will validate the project exists and is not default)
         self.config_manager.remove_project(name)
 
-        # Then remove from database
-        project = await self.repository.get_by_name(name)
+        # Then remove from database using robust lookup
+        project = await self.get_project(name)
         if project:
             await self.repository.delete(project.id)
 
@@ -161,8 +161,8 @@ class ProjectService:
         # First update config file (this will validate the project exists)
         self.config_manager.set_default_project(name)
 
-        # Then update database
-        project = await self.repository.get_by_name(name)
+        # Then update database using the same lookup logic as get_project
+        project = await self.get_project(name)
         if project:
             await self.repository.set_as_default(project.id)
         else:
@@ -323,7 +323,7 @@ class ProjectService:
             raise ValueError("Repository is required for move_project")
 
         # Resolve to absolute path
-        resolved_path = os.path.abspath(os.path.expanduser(new_path))
+        resolved_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
 
         # Validate project exists in config
         if name not in self.config_manager.projects:
@@ -338,8 +338,8 @@ class ProjectService:
         config.projects[name] = resolved_path
         self.config_manager.save_config(config)
 
-        # Update in database
-        project = await self.repository.get_by_name(name)
+        # Update in database using robust lookup
+        project = await self.get_project(name)
         if project:
             await self.repository.update_path(project.id, resolved_path)
             logger.info(f"Moved project '{name}' from {old_path} to {resolved_path}")
@@ -370,15 +370,15 @@ class ProjectService:
         if name not in self.config_manager.projects:
             raise ValueError(f"Project '{name}' not found in configuration")
 
-        # Get project from database
-        project = await self.repository.get_by_name(name)
+        # Get project from database using robust lookup
+        project = await self.get_project(name)
         if not project:
             logger.error(f"Project '{name}' exists in config but not in database")
             return
 
         # Update path if provided
         if updated_path:
-            resolved_path = os.path.abspath(os.path.expanduser(updated_path))
+            resolved_path = Path(os.path.abspath(os.path.expanduser(updated_path))).as_posix()
 
             # Update in config
             config = self.config_manager.load_config()

src/basic_memory/sync/sync_service.py

@@ -357,8 +357,8 @@ class SyncService:
 
             # get file timestamps
             file_stats = self.file_service.file_stats(path)
-            created = datetime.fromtimestamp(file_stats.st_ctime)
-            modified = datetime.fromtimestamp(file_stats.st_mtime)
+            created = datetime.fromtimestamp(file_stats.st_ctime).astimezone()
+            modified = datetime.fromtimestamp(file_stats.st_mtime).astimezone()
 
             # get mime type
             content_type = self.file_service.content_type(path)
@@ -619,7 +619,7 @@ class SyncService:
                     continue
 
                 path = Path(root) / filename
-                rel_path = str(path.relative_to(directory))
+                rel_path = path.relative_to(directory).as_posix()
                 checksum = await self.file_service.compute_checksum(rel_path)
                 result.files[rel_path] = checksum
                 result.checksums[checksum] = rel_path

src/basic_memory/sync/watch_service.py

@@ -197,7 +197,7 @@ class WatchService:
 
         for change, path in changes:
             # convert to relative path
-            relative_path = str(Path(path).relative_to(directory))
+            relative_path = Path(path).relative_to(directory).as_posix()
 
             # Skip .tmp files - they're temporary and shouldn't be synced
             if relative_path.endswith(".tmp"):
@@ -284,13 +284,36 @@ class WatchService:
         # Process deletes
         for path in deletes:
             if path not in processed:
-                logger.debug("Processing deleted file", path=path)
-                await sync_service.handle_delete(path)
-                self.state.add_event(path=path, action="deleted", status="success")
-                self.console.print(f"[red]✕[/red] {path}")
-                logger.info(f"deleted: {path}")
-                processed.add(path)
-                delete_count += 1
+                # Check if file still exists on disk (vim atomic write edge case)
+                full_path = directory / path
+                if full_path.exists() and full_path.is_file():
+                    # File still exists despite DELETE event - treat as modification
+                    logger.debug("File exists despite DELETE event, treating as modification", path=path)
+                    entity, checksum = await sync_service.sync_file(path, new=False)
+                    self.state.add_event(path=path, action="modified", status="success", checksum=checksum)
+                    self.console.print(f"[yellow]✎[/yellow] {path} (atomic write)")
+                    logger.info(f"atomic write detected: {path}")
+                    processed.add(path)
+                    modify_count += 1
+                else:
+                    # Check if this was a directory - skip if so
+                    # (we can't tell if the deleted path was a directory since it no longer exists,
+                    # so we check if there's an entity in the database for it)
+                    entity = await sync_service.entity_repository.get_by_file_path(path)
+                    if entity is None:
+                        # No entity means this was likely a directory - skip it
+                        logger.debug(f"Skipping deleted path with no entity (likely directory), path={path}")
+                        processed.add(path)
+                        continue
+                    
+                    # File truly deleted
+                    logger.debug("Processing deleted file", path=path)
+                    await sync_service.handle_delete(path)
+                    self.state.add_event(path=path, action="deleted", status="success")
+                    self.console.print(f"[red]✕[/red] {path}")
+                    logger.info(f"deleted: {path}")
+                    processed.add(path)
+                    delete_count += 1
 
         # Process adds
         for path in adds:

src/basic_memory/utils.py

@@ -4,11 +4,13 @@ import os
 
 import logging
 import re
-import unicodedata
+import sys
+from datetime import datetime
 from pathlib import Path
-from typing import Optional, Protocol, Union, runtime_checkable, List, Any
+from typing import Optional, Protocol, Union, runtime_checkable, List
 
 from loguru import logger
+from unidecode import unidecode
 
 
 @runtime_checkable
@@ -26,9 +28,11 @@ FilePath = Union[Path, str]
 logging.getLogger("opentelemetry.sdk.metrics._internal.instrument").setLevel(logging.ERROR)
 
 
-def generate_permalink(file_path: Union[Path, str, Any]) -> str:
-    """
-    Generate a permalink from a file path.
+def generate_permalink(file_path: Union[Path, str, PathLike], split_extension: bool = True) -> str:
+    """Generate a stable permalink from a file path.
+
+    Args:
+        file_path: Original file path (str, Path, or PathLike)
 
     Returns:
         Normalized permalink that matches validation rules. Converts spaces and underscores
@@ -37,7 +41,7 @@ def generate_permalink(file_path: Union[Path, str, Any]) -> str:
     Examples:
         >>> generate_permalink("docs/My Feature.md")
         'docs/my-feature'
-        >>> generate_permalink("specs/API_v2.md")
+        >>> generate_permalink("specs/API (v2).md")
         'specs/api-v2'
         >>> generate_permalink("design/unified_model_refactor.md")
         'design/unified-model-refactor'
@@ -45,84 +49,99 @@ def generate_permalink(file_path: Union[Path, str, Any]) -> str:
         '中文/测试文档'
     """
     # Convert Path to string if needed
-    path_str = str(file_path)
+    path_str = Path(str(file_path)).as_posix()
 
-    # Remove extension
-    base = os.path.splitext(path_str)[0]
+    # Remove extension (for now, possibly)
+    (base, extension) = os.path.splitext(path_str)
 
-    # Create a transliteration mapping for specific characters
-    transliteration_map = {
-        "ø": "o",  # Handle Søren -> soren
-        "å": "a",  # Handle Kierkegård -> kierkegard
-        "ü": "u",  # Handle Müller -> muller
-        "é": "e",  # Handle Café -> cafe
-        "è": "e",  # Handle Mère -> mere
-        "ê": "e",  # Handle Fête -> fete
-        "à": "a",  # Handle À la mode -> a la mode
-        "ç": "c",  # Handle Façade -> facade
-        "ñ": "n",  # Handle Niño -> nino
-        "ö": "o",  # Handle Björk -> bjork
-        "ä": "a",  # Handle Häagen -> haagen
-        # Add more mappings as needed
-    }
-
-    # Process character by character, transliterating Latin characters with diacritics
-    result = ""
-    for char in base:
-        # Direct mapping for known characters
-        if char.lower() in transliteration_map:
-            result += transliteration_map[char.lower()]
-        # General case using Unicode normalization
-        elif unicodedata.category(char).startswith("L") and ord(char) > 127:
-            # Decompose the character (e.g., ü -> u + combining diaeresis)
-            decomposed = unicodedata.normalize("NFD", char)
-            # If decomposition produced multiple characters and first one is ASCII
-            if len(decomposed) > 1 and ord(decomposed[0]) < 128:
-                # Keep only the base character
-                result += decomposed[0].lower()
-            else:
-                # For non-Latin scripts like Chinese, preserve the character
-                result += char
-        else:
-            # Add the character as is
-            result += char
-
-    # Handle special punctuation cases for apostrophes
-    result = result.replace("'", "")
-
-    # Insert dash between camelCase
-    # This regex finds boundaries between lowercase and uppercase letters
-    result = re.sub(r"([a-z0-9])([A-Z])", r"\1-\2", result)
-
-    # Insert dash between Chinese and Latin character boundaries
-    # This is needed for cases like "中文English" -> "中文-english"
-    result = re.sub(r"([\u4e00-\u9fff])([a-zA-Z])", r"\1-\2", result)
-    result = re.sub(r"([a-zA-Z])([\u4e00-\u9fff])", r"\1-\2", result)
-
-    # Convert ASCII letters to lowercase, preserve non-ASCII characters
-    lower_text = "".join(c.lower() if c.isascii() and c.isalpha() else c for c in result)
-
-    # Replace underscores with hyphens
-    text_with_hyphens = lower_text.replace("_", "-")
-
-    # Replace spaces and unsafe ASCII characters with hyphens, but preserve non-ASCII characters
-    # Include common Chinese character ranges and other non-ASCII characters
-    clean_text = re.sub(
-        r"[^a-z0-9\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf/\-]", "-", text_with_hyphens
+    # Check if we have CJK characters that should be preserved
+    # CJK ranges: \u4e00-\u9fff (CJK Unified Ideographs), \u3000-\u303f (CJK symbols),
+    # \u3400-\u4dbf (CJK Extension A), \uff00-\uffef (Fullwidth forms)
+    has_cjk_chars = any(
+        "\u4e00" <= char <= "\u9fff"
+        or "\u3000" <= char <= "\u303f"
+        or "\u3400" <= char <= "\u4dbf"
+        or "\uff00" <= char <= "\uffef"
+        for char in base
     )
 
+    if has_cjk_chars:
+        # For text with CJK characters, selectively transliterate only Latin accented chars
+        result = ""
+        for char in base:
+            if (
+                "\u4e00" <= char <= "\u9fff"
+                or "\u3000" <= char <= "\u303f"
+                or "\u3400" <= char <= "\u4dbf"
+            ):
+                # Preserve CJK ideographs and symbols
+                result += char
+            elif "\uff00" <= char <= "\uffef":
+                # Remove Chinese fullwidth punctuation entirely (like ，！？)
+                continue
+            else:
+                # Transliterate Latin accented characters to ASCII
+                result += unidecode(char)
+
+        # Insert hyphens between CJK and Latin character transitions
+        # Match: CJK followed by Latin letter/digit, or Latin letter/digit followed by CJK
+        result = re.sub(
+            r"([\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf])([a-zA-Z0-9])", r"\1-\2", result
+        )
+        result = re.sub(
+            r"([a-zA-Z0-9])([\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf])", r"\1-\2", result
+        )
+
+        # Insert dash between camelCase
+        result = re.sub(r"([a-z0-9])([A-Z])", r"\1-\2", result)
+
+        # Convert ASCII letters to lowercase, preserve CJK
+        lower_text = "".join(c.lower() if c.isascii() and c.isalpha() else c for c in result)
+
+        # Replace underscores with hyphens
+        text_with_hyphens = lower_text.replace("_", "-")
+
+        # Remove apostrophes entirely (don't replace with hyphens)
+        text_no_apostrophes = text_with_hyphens.replace("'", "")
+
+        # Replace unsafe chars with hyphens, but preserve CJK characters
+        clean_text = re.sub(
+            r"[^a-z0-9\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf/\-]", "-", text_no_apostrophes
+        )
+    else:
+        # Original ASCII-only processing for backward compatibility
+        # Transliterate unicode to ascii
+        ascii_text = unidecode(base)
+
+        # Insert dash between camelCase
+        ascii_text = re.sub(r"([a-z0-9])([A-Z])", r"\1-\2", ascii_text)
+
+        # Convert to lowercase
+        lower_text = ascii_text.lower()
+
+        # replace underscores with hyphens
+        text_with_hyphens = lower_text.replace("_", "-")
+
+        # 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)
+
     # Collapse multiple hyphens
     clean_text = re.sub(r"-+", "-", clean_text)
 
-    # Remove hyphens between adjacent Chinese characters only
-    # This handles cases like "你好-世界" -> "你好世界"
-    clean_text = re.sub(r"([\u4e00-\u9fff])-([\u4e00-\u9fff])", r"\1\2", clean_text)
-
     # Clean each path segment
     segments = clean_text.split("/")
     clean_segments = [s.strip("-") for s in segments]
 
-    return "/".join(clean_segments)
+    return_val = "/".join(clean_segments)
+
+    # Append file extension back, if necessary
+    if not split_extension and extension:
+        return_val += extension
+
+    return return_val
 
 
 def setup_logging(
@@ -143,7 +162,7 @@ def setup_logging(
         console: Whether to log to the console
     """
     # Remove default handler and any existing handlers
-    # logger.remove()
+    logger.remove()
 
     # Add file handler if we are not running tests and a log file is specified
     if log_file and env != "test":
@@ -161,8 +180,8 @@ def setup_logging(
         )
 
     # Add console logger if requested or in test mode
-    # if env == "test" or console:
-    #     logger.add(sys.stderr, level=log_level, backtrace=True, diagnose=True, colorize=True)
+    if env == "test" or console:
+        logger.add(sys.stderr, level=log_level, backtrace=True, diagnose=True, colorize=True)
 
     logger.info(f"ENV: '{env}' Log level: '{log_level}' Logging to {log_file}")
 
@@ -172,8 +191,6 @@ def setup_logging(
         "httpx": logging.WARNING,
         # File watching logs
         "watchfiles.main": logging.WARNING,
-        # SQLAlchemy deprecation warnings
-        "sqlalchemy": logging.WARNING,
     }
 
     # Set log levels for noisy loggers
@@ -181,6 +198,65 @@ def setup_logging(
         logging.getLogger(logger_name).setLevel(level)
 
 
+def parse_tags(tags: Union[List[str], str, None]) -> List[str]:
+    """Parse tags from various input formats into a consistent list.
+
+    Args:
+        tags: Can be a list of strings, a comma-separated string, or None
+
+    Returns:
+        A list of tag strings, or an empty list if no tags
+
+    Note:
+        This function strips leading '#' characters from tags to prevent
+        their accumulation when tags are processed multiple times.
+    """
+    if tags is None:
+        return []
+
+    # Process list of tags
+    if isinstance(tags, list):
+        # First strip whitespace, then strip leading '#' characters to prevent accumulation
+        return [tag.strip().lstrip("#") for tag in tags if tag and tag.strip()]
+
+    # Process string input
+    if isinstance(tags, str):
+        # Check if it's a JSON array string (common issue from AI assistants)
+        import json
+        if tags.strip().startswith('[') and tags.strip().endswith(']'):
+            try:
+                # Try to parse as JSON array
+                parsed_json = json.loads(tags)
+                if isinstance(parsed_json, list):
+                    # Recursively parse the JSON array as a list
+                    return parse_tags(parsed_json)
+            except json.JSONDecodeError:
+                # Not valid JSON, fall through to comma-separated parsing
+                pass
+        
+        # Split by comma, strip whitespace, then strip leading '#' characters
+        return [tag.strip().lstrip("#") for tag in tags.split(",") if tag and tag.strip()]
+
+    # For any other type, try to convert to string and parse
+    try:  # pragma: no cover
+        return parse_tags(str(tags))
+    except (ValueError, TypeError):  # pragma: no cover
+        logger.warning(f"Couldn't parse tags from input of type {type(tags)}: {tags}")
+        return []
+
+
+def normalize_newlines(multiline: str) -> str:
+    """Replace any \r\n, \r, or \n with the native newline.
+
+    Args:
+        multiline: String containing any mixture of newlines.
+
+    Returns:
+        A string with normalized newlines native to the platform.
+    """
+    return re.sub(r"\r\n?|\n", os.linesep, multiline)
+
+
 def normalize_file_path_for_comparison(file_path: str) -> str:
     """Normalize a file path for conflict detection.
 
@@ -254,40 +330,6 @@ def detect_potential_file_conflicts(file_path: str, existing_paths: List[str]) -
     return conflicts
 
 
-def parse_tags(tags: Union[List[str], str, None]) -> List[str]:
-    """Parse tags from various input formats into a consistent list.
-
-    Args:
-        tags: Can be a list of strings, a comma-separated string, or None
-
-    Returns:
-        A list of tag strings, or an empty list if no tags
-
-    Note:
-        This function strips leading '#' characters from tags to prevent
-        their accumulation when tags are processed multiple times.
-    """
-    if tags is None:
-        return []
-
-    # Process list of tags
-    if isinstance(tags, list):
-        # First strip whitespace, then strip leading '#' characters to prevent accumulation
-        return [tag.strip().lstrip("#") for tag in tags if tag and tag.strip()]
-
-    # Process comma-separated string of tags
-    if isinstance(tags, str):
-        # Split by comma, strip whitespace, then strip leading '#' characters
-        return [tag.strip().lstrip("#") for tag in tags.split(",") if tag and tag.strip()]
-
-    # For any other type, try to convert to string and parse
-    try:  # pragma: no cover
-        return parse_tags(str(tags))
-    except (ValueError, TypeError):  # pragma: no cover
-        logger.warning(f"Couldn't parse tags from input of type {type(tags)}: {tags}")
-        return []
-
-
 def validate_project_path(path: str, project_path: Path) -> bool:
     """Ensure path stays within project boundaries."""
     # Allow empty strings as they resolve to the project root
@@ -315,3 +357,23 @@ def validate_project_path(path: str, project_path: Path) -> bool:
         return resolved.is_relative_to(project_path.resolve())
     except (ValueError, OSError):
         return False
+
+
+def ensure_timezone_aware(dt: datetime) -> datetime:
+    """Ensure a datetime is timezone-aware using system timezone.
+
+    If the datetime is naive, convert it to timezone-aware using the system's local timezone.
+    If it's already timezone-aware, return it unchanged.
+
+    Args:
+        dt: The datetime to ensure is timezone-aware
+
+    Returns:
+        A timezone-aware datetime
+    """
+    if dt.tzinfo is None:
+        # Naive datetime - assume it's in local time and add timezone
+        return dt.astimezone()
+    else:
+        # Already timezone-aware
+        return dt

test-int/mcp/test_list_directory_integration.py

@@ -465,3 +465,79 @@ async def test_list_directory_complex_glob_patterns(mcp_server, app):
         assert "Project Beta Plan.md" in list_text
         assert "Meeting Minutes" not in list_text
         assert "matching 'Project*'" in list_text
+
+
+@pytest.mark.asyncio
+async def test_list_directory_dot_slash_prefix_paths(mcp_server, app):
+    """Test directory listing with ./ prefix paths (reproduces bug report issue)."""
+
+    async with Client(mcp_server) as client:
+        # Create test files in a subdirectory
+        await client.call_tool(
+            "write_note",
+            {
+                "title": "Artifact One",
+                "folder": "artifacts",
+                "content": "# Artifact One\n\nFirst artifact document.",
+                "tags": "artifact,test",
+            },
+        )
+
+        await client.call_tool(
+            "write_note",
+            {
+                "title": "Artifact Two",
+                "folder": "artifacts",
+                "content": "# Artifact Two\n\nSecond artifact document.",
+                "tags": "artifact,test",
+            },
+        )
+
+        # Test normal path without ./ prefix (should work)
+        normal_result = await client.call_tool(
+            "list_directory",
+            {
+                "dir_name": "artifacts",
+                "depth": 1,
+            },
+        )
+
+        assert len(normal_result.content) == 1
+        normal_text = normal_result.content[0].text
+        assert "Artifact One.md" in normal_text
+        assert "Artifact Two.md" in normal_text
+        assert "2 files" in normal_text
+
+        # Test with ./ prefix (this was the failing case in the bug report)
+        dot_slash_result = await client.call_tool(
+            "list_directory",
+            {
+                "dir_name": "./artifacts",
+                "depth": 1,
+            },
+        )
+
+        assert len(dot_slash_result.content) == 1
+        dot_slash_text = dot_slash_result.content[0].text
+
+        # Should show the same files as normal path
+        assert "Artifact One.md" in dot_slash_text
+        assert "Artifact Two.md" in dot_slash_text
+        assert "2 files" in dot_slash_text
+
+        # Test with trailing slash after ./ prefix
+        dot_slash_trailing_result = await client.call_tool(
+            "list_directory",
+            {
+                "dir_name": "./artifacts/",
+                "depth": 1,
+            },
+        )
+
+        assert len(dot_slash_trailing_result.content) == 1
+        dot_slash_trailing_text = dot_slash_trailing_result.content[0].text
+
+        # Should show the same files
+        assert "Artifact One.md" in dot_slash_trailing_text
+        assert "Artifact Two.md" in dot_slash_trailing_text
+        assert "2 files" in dot_slash_trailing_text

test-int/mcp/test_project_management_integration.py

@@ -604,15 +604,15 @@ async def test_create_delete_project_edge_cases(mcp_server, app):
     """Test edge cases for create and delete project operations."""
 
     async with Client(mcp_server) as client:
-        # Test with special characters in project name (should be handled gracefully)
-        special_name = "test-project-with-dashes"
+        # Test with special characters and spaces in project name (should be handled gracefully)
+        special_name = "test project with spaces & symbols!"
 
         # Create project with special characters
         create_result = await client.call_tool(
             "create_memory_project",
             {
                 "project_name": special_name,
-                "project_path": f"/tmp/{special_name}",
+                "project_path": "/tmp/test-project-with-special-chars",
             },
         )
         assert "✓" in create_result.content[0].text

test-int/mcp/test_write_note_integration.py

@@ -9,6 +9,9 @@ from textwrap import dedent
 
 import pytest
 from fastmcp import Client
+from unittest.mock import patch
+
+from basic_memory.config import ConfigManager
 
 
 @pytest.mark.asyncio
@@ -282,3 +285,64 @@ async def test_write_note_preserve_frontmatter(mcp_server, app):
         assert "# Created note" in response_text
         assert "file_path: test/Frontmatter Note.md" in response_text
         assert "permalink: test/frontmatter-note" in response_text
+
+
+@pytest.mark.asyncio
+async def test_write_note_kebab_filenames_basic(mcp_server):
+    """Test note creation with kebab_filenames=True and invalid filename characters."""
+
+    config = ConfigManager().config
+    curr_config_val = config.kebab_filenames
+    config.kebab_filenames = True
+
+    with patch.object(ConfigManager, "config", config):
+        async with Client(mcp_server) as client:
+            result = await client.call_tool(
+                "write_note",
+                {
+                    "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
+
+            # File path and permalink should be kebab-case and sanitized
+            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
+
+    # Restore original config value
+    config.kebab_filenames = curr_config_val
+
+
+@pytest.mark.asyncio
+async def test_write_note_kebab_filenames_repeat_invalid(mcp_server):
+    """Test note creation with multiple invalid and repeated characters."""
+
+    config = ConfigManager().config
+    curr_config_val = config.kebab_filenames
+    config.kebab_filenames = True
+
+    with patch.object(ConfigManager, "config", config):
+        async with Client(mcp_server) as client:
+            result = await client.call_tool(
+                "write_note",
+                {
+                    "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
+
+            assert "file_path: my-folder/crazy-note-name.md" in response_text
+            assert "permalink: my-folder/crazy-note-name" in response_text
+
+    # Restore original config value
+    config.kebab_filenames = curr_config_val

tests/api/test_knowledge_router.py

@@ -10,6 +10,7 @@ from basic_memory.schemas import (
     EntityResponse,
 )
 from basic_memory.schemas.search import SearchItemType, SearchResponse
+from basic_memory.utils import normalize_newlines
 
 
 @pytest.mark.asyncio
@@ -188,6 +189,7 @@ async def test_get_entity_by_permalink(client: AsyncClient, project_url):
     # Verify retrieval
     assert response.status_code == 200
     entity = response.json()
+    assert entity["title"] == "TestEntity"
     assert entity["file_path"] == "test/TestEntity.md"
     assert entity["entity_type"] == "test"
     assert entity["permalink"] == "test/test-entity"
@@ -209,6 +211,7 @@ async def test_get_entity_by_file_path(client: AsyncClient, project_url):
     # Verify retrieval
     assert response.status_code == 200
     entity = response.json()
+    assert entity["title"] == "TestEntity"
     assert entity["file_path"] == "test/TestEntity.md"
     assert entity["entity_type"] == "test"
     assert entity["permalink"] == "test/test-entity"
@@ -684,14 +687,14 @@ async def test_edit_entity_prepend(client: AsyncClient, project_url):
     file_content = response.text
 
     # Expected content with frontmatter preserved and content prepended to body
-    expected_content = """---
+    expected_content = normalize_newlines("""---
 title: Test Note
 type: note
 permalink: test/test-note
 ---
 
 Prepended content
-Original content"""
+Original content""")
 
     assert file_content.strip() == expected_content.strip()
 

tests/api/test_project_router.py

@@ -168,8 +168,8 @@ async def test_update_project_path_endpoint(
     """Test the update project endpoint for changing project path."""
     # Create a test project to update
     test_project_name = "test-update-project"
-    old_path = str(tmp_path / "old-location")
-    new_path = str(tmp_path / "new-location")
+    old_path = (tmp_path / "old-location").as_posix()
+    new_path = (tmp_path / "new-location").as_posix()
 
     await project_service.add_project(test_project_name, old_path)
 
@@ -256,8 +256,8 @@ async def test_update_project_both_params_endpoint(
     """Test the update project endpoint with both path and is_active parameters."""
     # Create a test project to update
     test_project_name = "test-update-both-project"
-    old_path = str(tmp_path / "old-location")
-    new_path = str(tmp_path / "new-location")
+    old_path = (tmp_path / "old-location").as_posix()
+    new_path = (tmp_path / "new-location").as_posix()
 
     await project_service.add_project(test_project_name, old_path)
 
@@ -344,7 +344,8 @@ async def test_update_project_no_params_endpoint(test_config, client, project_se
     await project_service.add_project(test_project_name, test_path)
     proj_info = await project_service.get_project(test_project_name)
     assert proj_info.name == test_project_name
-    assert proj_info.path == test_path
+    # On Windows the path is prepended with a drive letter
+    assert test_path in proj_info.path
 
     try:
         # Try to update with no parameters
@@ -354,7 +355,8 @@ async def test_update_project_no_params_endpoint(test_config, client, project_se
         assert response.status_code == 200
         proj_info = await project_service.get_project(test_project_name)
         assert proj_info.name == test_project_name
-        assert proj_info.path == test_path
+        # On Windows the path is prepended with a drive letter
+        assert test_path in proj_info.path
 
     finally:
         # Clean up

tests/api/test_resource_router.py

@@ -7,6 +7,7 @@ from pathlib import Path
 import pytest
 
 from basic_memory.schemas import EntityResponse
+from basic_memory.utils import normalize_newlines
 
 
 @pytest.mark.asyncio
@@ -35,7 +36,7 @@ async def test_get_resource_content(client, project_config, entity_repository, p
     response = await client.get(f"{project_url}/resource/{entity.permalink}")
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
-    assert response.text == content
+    assert response.text == normalize_newlines(content)
 
 
 @pytest.mark.asyncio
@@ -66,7 +67,7 @@ async def test_get_resource_pagination(client, project_config, entity_repository
     )
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
-    assert response.text == content
+    assert response.text == normalize_newlines(content)
 
 
 @pytest.mark.asyncio
@@ -148,7 +149,7 @@ async def test_get_resource_observation(client, project_config, entity_repositor
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
     assert (
-        """
+        normalize_newlines("""
 ---
 title: Test Entity
 type: test
@@ -158,7 +159,7 @@ permalink: test/test-entity
 # Test Content
 
 - [note] an observation.
-    """.strip()
+    """.strip())
         in response.text
     )
 
@@ -196,7 +197,7 @@ async def test_get_resource_entities(client, project_config, entity_repository,
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
     assert (
-        f"""
+        normalize_newlines(f"""
 --- memory://test/test-entity {entity1.updated_at.isoformat()} {entity1.checksum[:8]}
 
 # Test Content
@@ -206,7 +207,7 @@ async def test_get_resource_entities(client, project_config, entity_repository,
 # Related Content
 - links to [[Test Entity]]
 
-    """.strip()
+    """.strip())
         in response.text
     )
 
@@ -249,7 +250,7 @@ async def test_get_resource_entities_pagination(
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
     assert (
-        """
+        normalize_newlines("""
 ---
 title: Related Entity
 type: test
@@ -258,7 +259,7 @@ permalink: test/related-entity
 
 # Related Content
 - links to [[Test Entity]]
-""".strip()
+""".strip())
         in response.text
     )
 
@@ -297,7 +298,7 @@ async def test_get_resource_relation(client, project_config, entity_repository,
     assert response.status_code == 200
     assert response.headers["content-type"] == "text/markdown; charset=utf-8"
     assert (
-        f"""
+        normalize_newlines(f"""
 --- memory://test/test-entity {entity1.updated_at.isoformat()} {entity1.checksum[:8]}
 
 # Test Content
@@ -307,7 +308,7 @@ async def test_get_resource_relation(client, project_config, entity_repository,
 # Related Content
 - links to [[Test Entity]]
     
-    """.strip()
+    """.strip())
         in response.text
     )
 

tests/cli/test_cli_tools.py

@@ -309,7 +309,7 @@ def test_build_context_with_options(cli_env, setup_test_note):
     # Check that metadata reflects our options
     assert context_result["metadata"]["depth"] == 2
     timeframe = datetime.fromisoformat(context_result["metadata"]["timeframe"])
-    assert datetime.now() - timeframe <= timedelta(days=2)  # don't bother about timezones
+    assert datetime.now().astimezone() - timeframe <= timedelta(days=2)  # Compare timezone-aware datetimes
 
     # Results should include our test note
     found = False
@@ -321,6 +321,41 @@ def test_build_context_with_options(cli_env, setup_test_note):
     assert found, "Context did not include the test note"
 
 
+def test_build_context_string_depth_parameter(cli_env, setup_test_note):
+    """Test build_context command handles string depth parameter correctly."""
+    permalink = setup_test_note["permalink"]
+
+    # Test valid string depth parameter - Typer should convert it to int
+    result = runner.invoke(
+        tool_app,
+        [
+            "build-context",
+            f"memory://{permalink}",
+            "--depth",
+            "2",  # This is always a string from CLI
+        ],
+    )
+    assert result.exit_code == 0
+
+    # Result should be JSON containing our test note with correct depth
+    context_result = json.loads(result.stdout)
+    assert context_result["metadata"]["depth"] == 2
+
+    # Test invalid string depth parameter - should fail with Typer validation error
+    result = runner.invoke(
+        tool_app,
+        [
+            "build-context",
+            f"memory://{permalink}",
+            "--depth",
+            "invalid",
+        ],
+    )
+    assert result.exit_code == 2  # Typer exits with code 2 for parameter validation errors
+    # Typer should show a usage error for invalid integer
+    assert "invalid" in result.stderr and "is not a valid" in result.stderr and "integer" in result.stderr
+
+
 # The get-entity CLI command was removed when tools were refactored
 # into separate files with improved error handling
 

tests/cli/test_project_commands.py

@@ -85,7 +85,12 @@ def test_project_default_command(mock_reload, mock_run, cli_env):
     # Patching call_put directly since it's imported at the module level
 
     # Patch the os.environ for checking
-    with patch.dict(os.environ, {}, clear=True):
+    # On Windows, preserve USERPROFILE to allow home directory detection
+    env_vars = {}
+    if os.name == 'nt' and 'USERPROFILE' in os.environ:
+        env_vars['USERPROFILE'] = os.environ['USERPROFILE']
+
+    with patch.dict(os.environ, env_vars, clear=True):
         # Patch ConfigManager.set_default_project to prevent validation error
         with patch("basic_memory.config.ConfigManager.set_default_project"):
             runner = CliRunner()
@@ -179,3 +184,46 @@ def test_project_move_command_failure(mock_run, cli_env):
     # Should exit with code 1 and show error message
     assert result.exit_code == 1
     assert "Error moving project" in result.output
+
+
+@patch("basic_memory.cli.commands.project.call_patch")
+@patch("basic_memory.cli.commands.project.session")
+def test_project_move_command_uses_permalink(mock_session, mock_call_patch, cli_env):
+    """Test that the 'project move' command correctly generates and uses permalink in API call."""
+    # Mock the session to return a current project
+    mock_session.get_current_project.return_value = "current-project"
+    
+    # Mock successful API response
+    mock_response = MagicMock()
+    mock_response.status_code = 200
+    mock_response.json.return_value = {
+        "message": "Project 'Test Project Name' updated successfully",
+        "status": "success",
+        "default": False,
+    }
+    mock_call_patch.return_value = mock_response
+    
+    runner = CliRunner()
+    
+    # Test with a project name that needs normalization (spaces, mixed case)
+    project_name = "Test Project Name"
+    new_path = os.path.join("new", "path", "to", "project")
+    
+    result = runner.invoke(cli_app, ["project", "move", project_name, new_path])
+    
+    # Verify command executed successfully
+    assert result.exit_code == 0
+    
+    # Verify call_patch was called with the correct permalink-formatted project name
+    mock_call_patch.assert_called_once()
+    args, kwargs = mock_call_patch.call_args
+    
+    # Check the API endpoint uses the normalized permalink
+    expected_endpoint = "/current-project/project/test-project-name"
+    assert args[1] == expected_endpoint  # Second argument is the endpoint URL
+    
+    # Verify the data contains the resolved path (using same normalization as the function)
+    from pathlib import Path
+    expected_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
+    expected_data = {"path": expected_path}
+    assert kwargs["json"] == expected_data

tests/conftest.py

@@ -6,6 +6,7 @@ from pathlib import Path
 from textwrap import dedent
 from typing import AsyncGenerator
 
+import os
 import pytest
 import pytest_asyncio
 from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker
@@ -51,6 +52,9 @@ def project_root() -> Path:
 def config_home(tmp_path, monkeypatch) -> Path:
     # Patch HOME environment variable for the duration of the test
     monkeypatch.setenv("HOME", str(tmp_path))
+    # On Windows, also set USERPROFILE
+    if os.name == 'nt':
+        monkeypatch.setenv("USERPROFILE", str(tmp_path))
     # Set BASIC_MEMORY_HOME to the test directory
     monkeypatch.setenv("BASIC_MEMORY_HOME", str(tmp_path / "basic-memory"))
     return tmp_path

tests/db/test_issue_254_foreign_key_constraints.py

@@ -0,0 +1,154 @@
+"""Test to verify that issue #254 is fixed.
+
+Issue #254: Foreign key constraint failures when deleting projects with related entities.
+
+The issue was that when migration 647e7a75e2cd recreated the project table,
+it did not re-establish the foreign key constraint from entity.project_id to project.id
+with CASCADE DELETE, causing foreign key constraint failures when trying to delete
+projects that have related entities.
+
+Migration a1b2c3d4e5f6 was created to fix this by adding the missing foreign key
+constraint with CASCADE DELETE behavior.
+
+This test file verifies that the fix works correctly in production databases
+that have had the migration applied.
+"""
+from datetime import datetime, timezone
+
+import pytest
+
+from basic_memory.services.project_service import ProjectService
+
+
+#@pytest.mark.skip(reason="Issue #254 not fully resolved yet - foreign key constraint errors still occur")
+@pytest.mark.asyncio
+async def test_issue_254_foreign_key_constraint_fix(project_service: ProjectService, tmp_path):
+    """Test to verify issue #254 is fixed: project removal with foreign key constraints.
+    
+    This test reproduces the exact scenario from issue #254:
+    1. Create a project
+    2. Create entities, observations, and relations linked to that project  
+    3. Attempt to remove the project
+    4. Verify it succeeds without "FOREIGN KEY constraint failed" errors
+    5. Verify all related data is properly cleaned up via CASCADE DELETE
+    
+    Once issue #254 is fully fixed, remove the @pytest.mark.skip decorator.
+    """
+    test_project_name = "issue-254-verification"
+    test_project_path = str(tmp_path / "issue-254-verification")
+    
+    # Step 1: Create test project
+    await project_service.add_project(test_project_name, test_project_path)
+    project = await project_service.get_project(test_project_name)
+    assert project is not None, "Project should be created successfully"
+    
+    # Step 2: Create related entities that would cause foreign key constraint issues
+    from basic_memory.repository.entity_repository import EntityRepository
+    from basic_memory.repository.observation_repository import ObservationRepository
+    from basic_memory.repository.relation_repository import RelationRepository
+    
+    entity_repo = EntityRepository(project_service.repository.session_maker, project_id=project.id)
+    obs_repo = ObservationRepository(project_service.repository.session_maker, project_id=project.id)
+    rel_repo = RelationRepository(project_service.repository.session_maker, project_id=project.id)
+    
+    # Create entity
+    entity_data = {
+        "title": "Issue 254 Test Entity",
+        "entity_type": "note",
+        "content_type": "text/markdown",
+        "project_id": project.id,
+        "permalink": "issue-254-entity",
+        "file_path": "issue-254-entity.md",
+        "checksum": "issue254test",
+        "created_at": datetime.now(timezone.utc),
+        "updated_at": datetime.now(timezone.utc),
+    }
+    entity = await entity_repo.create(entity_data)
+    
+    # Create observation linked to entity
+    observation_data = {
+        "entity_id": entity.id,
+        "content": "This observation should be cascade deleted",
+        "category": "test"
+    }
+    observation = await obs_repo.create(observation_data)
+    
+    # Create relation involving the entity
+    relation_data = {
+        "from_id": entity.id,
+        "to_name": "some-other-entity",
+        "relation_type": "relates-to"
+    }
+    relation = await rel_repo.create(relation_data)
+    
+    # Step 3: Attempt to remove the project
+    # This is where issue #254 manifested - should NOT raise "FOREIGN KEY constraint failed"
+    try:
+        await project_service.remove_project(test_project_name)
+    except Exception as e:
+        if "FOREIGN KEY constraint failed" in str(e):
+            pytest.fail(
+                f"Issue #254 not fixed - foreign key constraint error still occurs: {e}. "
+                f"The migration a1b2c3d4e5f6 may not have been applied correctly or "
+                f"the CASCADE DELETE constraint is not working as expected."
+            )
+        else:
+            # Re-raise unexpected errors
+            raise
+    
+    # Step 4: Verify project was successfully removed
+    removed_project = await project_service.get_project(test_project_name)
+    assert removed_project is None, "Project should have been removed"
+    
+    # Step 5: Verify related data was cascade deleted
+    remaining_entity = await entity_repo.find_by_id(entity.id)
+    assert remaining_entity is None, "Entity should have been cascade deleted"
+    
+    remaining_observation = await obs_repo.find_by_id(observation.id)
+    assert remaining_observation is None, "Observation should have been cascade deleted"
+    
+    remaining_relation = await rel_repo.find_by_id(relation.id)
+    assert remaining_relation is None, "Relation should have been cascade deleted"
+
+
+@pytest.mark.asyncio
+async def test_issue_254_reproduction(project_service: ProjectService, tmp_path):
+    """Test that reproduces issue #254 to document the current state.
+    
+    This test demonstrates the current behavior and will fail until the issue is fixed.
+    It serves as documentation of what the problem was.
+    """
+    test_project_name = "issue-254-reproduction"
+    test_project_path = str(tmp_path / "issue-254-reproduction")
+    
+    # Create project and entity
+    await project_service.add_project(test_project_name, test_project_path)
+    project = await project_service.get_project(test_project_name)
+    
+    from basic_memory.repository.entity_repository import EntityRepository
+    entity_repo = EntityRepository(project_service.repository.session_maker, project_id=project.id)
+    
+    entity_data = {
+        "title": "Reproduction Entity",
+        "entity_type": "note",
+        "content_type": "text/markdown",
+        "project_id": project.id,
+        "permalink": "reproduction-entity",
+        "file_path": "reproduction-entity.md",
+        "checksum": "repro123",
+        "created_at": datetime.now(timezone.utc),
+        "updated_at": datetime.now(timezone.utc),
+    }
+    await entity_repo.create(entity_data)
+    
+    # This should eventually work without errors once issue #254 is fixed
+    #with pytest.raises(Exception) as exc_info:
+    await project_service.remove_project(test_project_name)
+    
+    # Document the current error for tracking
+    # error_message = str(exc_info.value)
+    # assert any(keyword in error_message for keyword in [
+    #     "FOREIGN KEY constraint failed",
+    #     "constraint",
+    #     "integrity"
+    # ]), f"Expected foreign key or integrity constraint error, got: {error_message}"

tests/markdown/test_markdown_plugins.py

@@ -75,6 +75,52 @@ def test_observation_edge_cases():
     assert not is_observation(token)
 
 
+def test_observation_excludes_markdown_and_wiki_links():
+    """Test that markdown links and wiki links are NOT parsed as observations.
+    
+    This test validates the fix for issue #247 where:
+    - [text](url) markdown links were incorrectly parsed as observations
+    - [[text]] wiki links were incorrectly parsed as observations
+    """
+    # Test markdown links are NOT observations
+    token = Token("inline", "[Click here](https://example.com)", 0)
+    assert not is_observation(token), "Markdown links should not be parsed as observations"
+    
+    token = Token("inline", "[Documentation](./docs/readme.md)", 0)  
+    assert not is_observation(token), "Relative markdown links should not be parsed as observations"
+    
+    token = Token("inline", "[Empty link]()", 0)
+    assert not is_observation(token), "Empty markdown links should not be parsed as observations"
+    
+    # Test wiki links are NOT observations
+    token = Token("inline", "[[SomeWikiPage]]", 0)
+    assert not is_observation(token), "Wiki links should not be parsed as observations"
+    
+    token = Token("inline", "[[Multi Word Page]]", 0)
+    assert not is_observation(token), "Multi-word wiki links should not be parsed as observations"
+    
+    # Test nested brackets are NOT observations
+    token = Token("inline", "[[Nested [[Inner]] Link]]", 0)
+    assert not is_observation(token), "Nested wiki links should not be parsed as observations"
+    
+    # Test valid observations still work (should return True)
+    token = Token("inline", "[category] This is a valid observation", 0)
+    assert is_observation(token), "Valid observations should still be parsed correctly"
+    
+    token = Token("inline", "[design] Valid observation #tag", 0)
+    assert is_observation(token), "Valid observations with tags should still work"
+    
+    token = Token("inline", "Just some text #tag", 0)
+    assert is_observation(token), "Tag-only observations should still work"
+    
+    # Test edge cases that should NOT be observations
+    token = Token("inline", "[]Empty brackets", 0)
+    assert not is_observation(token), "Empty category brackets should not be observations"
+    
+    token = Token("inline", "[category]No space after category", 0) 
+    assert not is_observation(token), "No space after category should not be valid observation"
+
+
 def test_relation_plugin():
     """Test relation plugin."""
     md = MarkdownIt().use(relation_plugin)

tests/mcp/test_obsidian_yaml_formatting.py

@@ -0,0 +1,181 @@
+"""Integration tests for Obsidian-compatible YAML formatting in write_note tool."""
+
+import pytest
+
+from basic_memory.mcp.tools import write_note
+
+
+@pytest.mark.asyncio
+async def test_write_note_tags_yaml_format(app, project_config):
+    """Test that write_note creates files with proper YAML list format for tags."""
+    # Create a note with tags using write_note
+    result = await write_note.fn(
+        title="YAML Format Test",
+        folder="test", 
+        content="Testing YAML tag formatting",
+        tags=["system", "overview", "reference"]
+    )
+    
+    # Verify the note was created successfully
+    assert "Created note" in result
+    assert "file_path: test/YAML Format Test.md" in result
+    
+    # Read the file directly to check YAML formatting
+    file_path = project_config.home / "test" / "YAML Format Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Should use YAML list format
+    assert "tags:" in content
+    assert "- system" in content
+    assert "- overview" in content
+    assert "- reference" in content
+    
+    # Should NOT use JSON array format
+    assert '["system"' not in content
+    assert '"overview"' not in content
+    assert '"reference"]' not in content
+
+
+@pytest.mark.asyncio  
+async def test_write_note_stringified_json_tags(app, project_config):
+    """Test that stringified JSON arrays are handled correctly."""
+    # This simulates the issue where AI assistants pass tags as stringified JSON
+    result = await write_note.fn(
+        title="Stringified JSON Test",
+        folder="test",
+        content="Testing stringified JSON tag input", 
+        tags='["python", "testing", "json"]'  # Stringified JSON array
+    )
+    
+    # Verify the note was created successfully
+    assert "Created note" in result
+    
+    # Read the file to check formatting
+    file_path = project_config.home / "test" / "Stringified JSON Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Should properly parse the JSON and format as YAML list
+    assert "tags:" in content
+    assert "- python" in content
+    assert "- testing" in content
+    assert "- json" in content
+    
+    # Should NOT have the original stringified format issues
+    assert '["python"' not in content
+    assert '"testing"' not in content
+    assert '"json"]' not in content
+
+
+@pytest.mark.asyncio
+async def test_write_note_single_tag_yaml_format(app, project_config):
+    """Test that single tags are still formatted as YAML lists."""
+    await write_note.fn(
+        title="Single Tag Test",
+        folder="test",
+        content="Testing single tag formatting",
+        tags=["solo-tag"]
+    )
+    
+    file_path = project_config.home / "test" / "Single Tag Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Single tag should still use list format
+    assert "tags:" in content
+    assert "- solo-tag" in content
+
+
+@pytest.mark.asyncio
+async def test_write_note_no_tags(app, project_config):
+    """Test that notes without tags work normally."""
+    await write_note.fn(
+        title="No Tags Test",
+        folder="test", 
+        content="Testing note without tags",
+        tags=None
+    )
+    
+    file_path = project_config.home / "test" / "No Tags Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Should not have tags field in frontmatter
+    assert "tags:" not in content
+    assert "title: No Tags Test" in content
+
+
+@pytest.mark.asyncio
+async def test_write_note_empty_tags_list(app, project_config):
+    """Test that empty tag lists are handled properly."""
+    await write_note.fn(
+        title="Empty Tags Test",
+        folder="test",
+        content="Testing empty tag list",
+        tags=[]
+    )
+    
+    file_path = project_config.home / "test" / "Empty Tags Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Should not add tags field to frontmatter for empty lists
+    assert "tags:" not in content
+    
+
+@pytest.mark.asyncio  
+async def test_write_note_update_preserves_yaml_format(app, project_config):
+    """Test that updating a note preserves the YAML list format."""
+    # First, create the note
+    await write_note.fn(
+        title="Update Format Test",
+        folder="test",
+        content="Initial content",
+        tags=["initial", "tag"]
+    )
+    
+    # Then update it with new tags
+    result = await write_note.fn(
+        title="Update Format Test", 
+        folder="test",
+        content="Updated content", 
+        tags=["updated", "new-tag", "format"]
+    )
+    
+    # Should be an update, not a new creation
+    assert "Updated note" in result
+    
+    # Check the file format
+    file_path = project_config.home / "test" / "Update Format Test.md" 
+    content = file_path.read_text(encoding="utf-8")
+    
+    # Should have proper YAML formatting for updated tags
+    assert "tags:" in content
+    assert "- updated" in content
+    assert "- new-tag" in content
+    assert "- format" in content
+    
+    # Old tags should be gone
+    assert "- initial" not in content
+    assert "- tag" not in content
+    
+    # Content should be updated
+    assert "Updated content" in content
+    assert "Initial content" not in content
+
+
+@pytest.mark.asyncio
+async def test_complex_tags_yaml_format(app, project_config):
+    """Test that complex tags with special characters format correctly."""
+    await write_note.fn(
+        title="Complex Tags Test",
+        folder="test",
+        content="Testing complex tag formats",
+        tags=["python-3.9", "api_integration", "v2.0", "nested/category", "under_score"]
+    )
+    
+    file_path = project_config.home / "test" / "Complex Tags Test.md"
+    content = file_path.read_text(encoding="utf-8")
+    
+    # All complex tags should format correctly
+    assert "- python-3.9" in content
+    assert "- api_integration" in content  
+    assert "- v2.0" in content
+    assert "- nested/category" in content
+    assert "- under_score" in content

tests/mcp/test_prompts.py

@@ -116,7 +116,7 @@ def test_prompt_context_with_file_path_no_permalink():
 
     # Create a mock context with a file that has no permalink (like a binary file)
     test_entity = EntitySummary(
-        type="file",
+        type="entity",
         title="Test File",
         permalink=None,  # No permalink
         file_path="test_file.pdf",

tests/mcp/test_tool_build_context.py

@@ -114,3 +114,23 @@ async def test_build_context_timeframe_formats(client, test_graph):
     for timeframe in invalid_timeframes:
         with pytest.raises(ToolError):
             await build_context.fn(url=test_url, timeframe=timeframe)
+
+
+@pytest.mark.asyncio
+async def test_build_context_string_depth_parameter(client, test_graph):
+    """Test that build_context handles string depth parameter correctly."""
+    test_url = "memory://test/root"
+    
+    # Test valid string depth parameter - should either raise ToolError or convert to int
+    try:
+        result = await build_context.fn(url=test_url, depth="2")
+        # If it succeeds, verify the depth was converted to an integer
+        assert isinstance(result.metadata.depth, int)
+        assert result.metadata.depth == 2
+    except ToolError:
+        # This is also acceptable behavior - type validation should catch it
+        pass
+    
+    # Test invalid string depth parameter - should raise ToolError
+    with pytest.raises(ToolError):
+        await build_context.fn(url=test_url, depth="invalid")

tests/mcp/test_tool_read_note.py

@@ -10,6 +10,7 @@ import pytest_asyncio
 from unittest.mock import MagicMock, patch
 
 from basic_memory.schemas.search import SearchResponse, SearchItemType
+from basic_memory.utils import normalize_newlines
 
 
 @pytest_asyncio.fixture
@@ -61,7 +62,7 @@ async def test_note_unicode_content(app):
 
     # Read back should preserve unicode
     result = await read_note.fn("test/unicode-test")
-    assert content in result
+    assert normalize_newlines(content) in result
 
 
 @pytest.mark.asyncio

tests/mcp/test_tool_write_note.py

@@ -4,6 +4,7 @@ from textwrap import dedent
 import pytest
 
 from basic_memory.mcp.tools import write_note, read_note, delete_note
+from basic_memory.utils import normalize_newlines
 
 
 @pytest.mark.asyncio
@@ -33,7 +34,7 @@ async def test_write_note(app):
     # Try reading it back via permalink
     content = await read_note.fn("test/test-note")
     assert (
-        dedent("""
+        normalize_newlines(dedent("""
         ---
         title: Test Note
         type: note
@@ -45,7 +46,7 @@ async def test_write_note(app):
         
         # Test
         This is a test note
-        """).strip()
+        """).strip())
         in content
     )
 
@@ -62,7 +63,7 @@ async def test_write_note_no_tags(app):
     # Should be able to read it back
     content = await read_note.fn("test/simple-note")
     assert (
-        dedent("""
+        normalize_newlines(dedent("""
         ---
         title: Simple Note
         type: note
@@ -70,7 +71,7 @@ async def test_write_note_no_tags(app):
         ---
         
         Just some text
-        """).strip()
+        """).strip())
         in content
     )
 
@@ -114,7 +115,7 @@ async def test_write_note_update_existing(app):
     # Try reading it back
     content = await read_note.fn("test/test-note")
     assert (
-        dedent(
+        normalize_newlines(dedent(
             """
         ---
         title: Test Note
@@ -128,7 +129,7 @@ async def test_write_note_update_existing(app):
         # Test
         This is an updated note
         """
-        ).strip()
+        ).strip())
         == content
     )
 
@@ -393,7 +394,7 @@ async def test_write_note_preserves_content_frontmatter(app):
     # Try reading it back via permalink
     content = await read_note.fn("test/test-note")
     assert (
-        dedent(
+        normalize_newlines(dedent(
             """
             ---
             title: Test Note
@@ -410,7 +411,7 @@ async def test_write_note_preserves_content_frontmatter(app):
             
             This is a test note
             """
-        ).strip()
+        ).strip())
         in content
     )
 
@@ -497,7 +498,7 @@ async def test_write_note_with_custom_entity_type(app):
     # Verify the entity type is correctly set in the frontmatter
     content = await read_note.fn("guides/test-guide")
     assert (
-        dedent("""
+        normalize_newlines(dedent("""
         ---
         title: Test Guide
         type: guide
@@ -509,7 +510,7 @@ async def test_write_note_with_custom_entity_type(app):
         
         # Guide Content
         This is a guide
-        """).strip()
+        """).strip())
         in content
     )
 

tests/repository/test_search_repository_edit_bug_fix.py

@@ -0,0 +1,270 @@
+"""Tests for the search repository edit bug fix.
+
+This test reproduces the critical bug where editing notes causes them to disappear
+from the search index due to missing project_id filter in index_item() method.
+"""
+
+from datetime import datetime, timezone
+
+import pytest
+import pytest_asyncio
+
+from basic_memory.models.project import Project
+from basic_memory.repository.search_repository import SearchRepository, SearchIndexRow
+from basic_memory.schemas.search import SearchItemType
+
+
+@pytest_asyncio.fixture
+async def second_test_project(project_repository):
+    """Create a second project for testing project isolation during edits."""
+    project_data = {
+        "name": "Second Edit Test Project",
+        "description": "Another project for testing edit bug",
+        "path": "/second/edit/test/path",
+        "is_active": True,
+        "is_default": None,
+    }
+    return await project_repository.create(project_data)
+
+
+@pytest_asyncio.fixture
+async def second_search_repo(session_maker, second_test_project):
+    """Create a search repository for the second project."""
+    return SearchRepository(session_maker, project_id=second_test_project.id)
+
+
+@pytest.mark.asyncio
+async def test_index_item_respects_project_isolation_during_edit():
+    """Test that index_item() doesn't delete records from other projects during edits.
+    
+    This test reproduces the critical bug where editing a note in one project
+    would delete search index entries with the same permalink from ALL projects,
+    causing notes to disappear from the search index.
+    """
+    from basic_memory import db
+    from basic_memory.models.base import Base
+    from basic_memory.repository.search_repository import SearchRepository
+    from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker
+
+    # Create a separate in-memory database for this test
+    engine = create_async_engine("sqlite+aiosqlite:///:memory:")
+    session_maker = async_sessionmaker(engine, expire_on_commit=False)
+    
+    # Create the database schema
+    async with engine.begin() as conn:
+        await conn.run_sync(Base.metadata.create_all)
+    
+    # Create two projects
+    async with db.scoped_session(session_maker) as session:
+        project1 = Project(
+            name="Project 1",
+            description="First project",
+            path="/project1/path",
+            is_active=True,
+            is_default=True
+        )
+        project2 = Project(
+            name="Project 2", 
+            description="Second project",
+            path="/project2/path",
+            is_active=True,
+            is_default=False
+        )
+        session.add(project1)
+        session.add(project2)
+        await session.flush()
+        
+        project1_id = project1.id
+        project2_id = project2.id
+        await session.commit()
+
+    # Create search repositories for both projects
+    repo1 = SearchRepository(session_maker, project_id=project1_id)
+    repo2 = SearchRepository(session_maker, project_id=project2_id)
+
+    # Initialize search index
+    await repo1.init_search_index()
+
+    # Create two notes with the SAME permalink in different projects
+    # This simulates the same note name/structure across different projects
+    same_permalink = "notes/test-note"
+    
+    search_row1 = SearchIndexRow(
+        id=1,
+        type=SearchItemType.ENTITY.value,
+        title="Test Note in Project 1",
+        content_stems="project 1 content original",
+        content_snippet="This is the original content in project 1",
+        permalink=same_permalink,
+        file_path="notes/test_note.md",
+        entity_id=1,
+        metadata={"entity_type": "note"},
+        created_at=datetime.now(timezone.utc),
+        updated_at=datetime.now(timezone.utc),
+        project_id=project1_id,
+    )
+
+    search_row2 = SearchIndexRow(
+        id=2,
+        type=SearchItemType.ENTITY.value,
+        title="Test Note in Project 2",
+        content_stems="project 2 content original",
+        content_snippet="This is the original content in project 2",
+        permalink=same_permalink,  # SAME permalink as project 1
+        file_path="notes/test_note.md",
+        entity_id=2,
+        metadata={"entity_type": "note"},
+        created_at=datetime.now(timezone.utc),
+        updated_at=datetime.now(timezone.utc),
+        project_id=project2_id,
+    )
+
+    # Index both items in their respective projects
+    await repo1.index_item(search_row1)
+    await repo2.index_item(search_row2)
+
+    # Verify both projects can find their respective notes
+    results1_before = await repo1.search(search_text="project 1 content")
+    assert len(results1_before) == 1
+    assert results1_before[0].title == "Test Note in Project 1"
+    assert results1_before[0].project_id == project1_id
+
+    results2_before = await repo2.search(search_text="project 2 content")
+    assert len(results2_before) == 1
+    assert results2_before[0].title == "Test Note in Project 2"
+    assert results2_before[0].project_id == project2_id
+
+    # Now simulate editing the note in project 1 (which re-indexes it)
+    # This would trigger the bug where the DELETE query doesn't filter by project_id
+    edited_search_row1 = SearchIndexRow(
+        id=1,
+        type=SearchItemType.ENTITY.value,
+        title="Test Note in Project 1",
+        content_stems="project 1 content EDITED",  # Changed content
+        content_snippet="This is the EDITED content in project 1",
+        permalink=same_permalink,
+        file_path="notes/test_note.md", 
+        entity_id=1,
+        metadata={"entity_type": "note"},
+        created_at=datetime.now(timezone.utc),
+        updated_at=datetime.now(timezone.utc),
+        project_id=project1_id,
+    )
+
+    # Re-index the edited note in project 1
+    # BEFORE THE FIX: This would delete the note from project 2 as well!
+    await repo1.index_item(edited_search_row1)
+
+    # Verify project 1 has the edited version
+    results1_after = await repo1.search(search_text="project 1 content EDITED")
+    assert len(results1_after) == 1
+    assert results1_after[0].title == "Test Note in Project 1"
+    assert "EDITED" in results1_after[0].content_snippet
+
+    # CRITICAL TEST: Verify project 2's note is still there (the bug would delete it)
+    results2_after = await repo2.search(search_text="project 2 content")
+    assert len(results2_after) == 1, "Project 2's note disappeared after editing project 1's note!"
+    assert results2_after[0].title == "Test Note in Project 2"
+    assert results2_after[0].project_id == project2_id
+    assert "original" in results2_after[0].content_snippet  # Should still be original
+
+    # Double-check: project 1 should not be able to see project 2's note
+    cross_search = await repo1.search(search_text="project 2 content")
+    assert len(cross_search) == 0
+
+    await engine.dispose()
+
+
+@pytest.mark.asyncio 
+async def test_index_item_updates_existing_record_same_project():
+    """Test that index_item() correctly updates existing records within the same project."""
+    from basic_memory import db
+    from basic_memory.models.base import Base
+    from basic_memory.repository.search_repository import SearchRepository
+    from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker
+
+    # Create a separate in-memory database for this test
+    engine = create_async_engine("sqlite+aiosqlite:///:memory:")
+    session_maker = async_sessionmaker(engine, expire_on_commit=False)
+    
+    # Create the database schema
+    async with engine.begin() as conn:
+        await conn.run_sync(Base.metadata.create_all)
+    
+    # Create one project
+    async with db.scoped_session(session_maker) as session:
+        project = Project(
+            name="Test Project",
+            description="Test project",
+            path="/test/path",
+            is_active=True,
+            is_default=True
+        )
+        session.add(project)
+        await session.flush()
+        project_id = project.id
+        await session.commit()
+
+    # Create search repository
+    repo = SearchRepository(session_maker, project_id=project_id)
+    await repo.init_search_index()
+
+    permalink = "test/my-note"
+
+    # Create initial note
+    initial_row = SearchIndexRow(
+        id=1,
+        type=SearchItemType.ENTITY.value,
+        title="My Test Note",
+        content_stems="initial content here",
+        content_snippet="This is the initial content",
+        permalink=permalink,
+        file_path="test/my_note.md",
+        entity_id=1,
+        metadata={"entity_type": "note"},
+        created_at=datetime.now(timezone.utc),
+        updated_at=datetime.now(timezone.utc),
+        project_id=project_id,
+    )
+
+    # Index the initial version
+    await repo.index_item(initial_row)
+
+    # Verify it exists
+    results_initial = await repo.search(search_text="initial content")
+    assert len(results_initial) == 1
+    assert results_initial[0].content_snippet == "This is the initial content"
+
+    # Now update the note (simulate an edit)
+    updated_row = SearchIndexRow(
+        id=1,
+        type=SearchItemType.ENTITY.value,
+        title="My Test Note",
+        content_stems="updated content here",  # Changed
+        content_snippet="This is the UPDATED content",  # Changed
+        permalink=permalink,  # Same permalink
+        file_path="test/my_note.md",
+        entity_id=1,
+        metadata={"entity_type": "note"},
+        created_at=datetime.now(timezone.utc),
+        updated_at=datetime.now(timezone.utc),
+        project_id=project_id,
+    )
+
+    # Re-index (should replace the old version)
+    await repo.index_item(updated_row)
+
+    # Verify the old version is gone
+    results_old = await repo.search(search_text="initial content")
+    assert len(results_old) == 0
+
+    # Verify the new version exists
+    results_new = await repo.search(search_text="updated content")
+    assert len(results_new) == 1
+    assert results_new[0].content_snippet == "This is the UPDATED content"
+
+    # Verify we only have one record (not duplicated)
+    all_results = await repo.search(search_text="My Test Note")
+    assert len(all_results) == 1
+
+    await engine.dispose()

tests/schemas/test_memory_serialization.py

@@ -0,0 +1,234 @@
+"""Tests for datetime serialization in memory schema models."""
+
+import json
+from datetime import datetime
+
+
+from basic_memory.schemas.memory import (
+    EntitySummary,
+    RelationSummary, 
+    ObservationSummary,
+    MemoryMetadata,
+    GraphContext,
+    ContextResult
+)
+
+
+class TestDateTimeSerialization:
+    """Test datetime serialization for MCP schema compliance."""
+
+    def test_entity_summary_datetime_serialization(self):
+        """Test EntitySummary serializes datetime as ISO format string."""
+        test_datetime = datetime(2023, 12, 8, 10, 30, 0)
+        
+        entity = EntitySummary(
+            permalink="test/entity",
+            title="Test Entity", 
+            file_path="test/entity.md",
+            created_at=test_datetime
+        )
+        
+        # Test model_dump_json() produces ISO format
+        json_str = entity.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["created_at"] == "2023-12-08T10:30:00"
+        assert data["type"] == "entity"
+        assert data["title"] == "Test Entity"
+
+    def test_relation_summary_datetime_serialization(self):
+        """Test RelationSummary serializes datetime as ISO format string."""
+        test_datetime = datetime(2023, 12, 8, 15, 45, 30)
+        
+        relation = RelationSummary(
+            title="Test Relation",
+            file_path="test/relation.md", 
+            permalink="test/relation",
+            relation_type="relates_to",
+            from_entity="entity1",
+            to_entity="entity2", 
+            created_at=test_datetime
+        )
+        
+        # Test model_dump_json() produces ISO format
+        json_str = relation.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["created_at"] == "2023-12-08T15:45:30"
+        assert data["type"] == "relation"
+        assert data["relation_type"] == "relates_to"
+
+    def test_observation_summary_datetime_serialization(self):
+        """Test ObservationSummary serializes datetime as ISO format string."""
+        test_datetime = datetime(2023, 12, 8, 20, 15, 45)
+        
+        observation = ObservationSummary(
+            title="Test Observation",
+            file_path="test/observation.md",
+            permalink="test/observation", 
+            category="note",
+            content="Test content",
+            created_at=test_datetime
+        )
+        
+        # Test model_dump_json() produces ISO format
+        json_str = observation.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["created_at"] == "2023-12-08T20:15:45"
+        assert data["type"] == "observation"
+        assert data["category"] == "note"
+
+    def test_memory_metadata_datetime_serialization(self):
+        """Test MemoryMetadata serializes datetime as ISO format string."""
+        test_datetime = datetime(2023, 12, 8, 12, 0, 0)
+        
+        metadata = MemoryMetadata(
+            depth=2,
+            generated_at=test_datetime,
+            primary_count=5,
+            related_count=3
+        )
+        
+        # Test model_dump_json() produces ISO format  
+        json_str = metadata.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["generated_at"] == "2023-12-08T12:00:00"
+        assert data["depth"] == 2
+        assert data["primary_count"] == 5
+
+    def test_context_result_with_datetime_serialization(self):
+        """Test ContextResult with nested models serializes datetime correctly."""
+        test_datetime = datetime(2023, 12, 8, 9, 30, 15)
+        
+        entity = EntitySummary(
+            permalink="test/entity",
+            title="Test Entity",
+            file_path="test/entity.md", 
+            created_at=test_datetime
+        )
+        
+        observation = ObservationSummary(
+            title="Test Observation",
+            file_path="test/observation.md",
+            permalink="test/observation",
+            category="note", 
+            content="Test content",
+            created_at=test_datetime
+        )
+        
+        context_result = ContextResult(
+            primary_result=entity,
+            observations=[observation],
+            related_results=[]
+        )
+        
+        # Test model_dump_json() produces ISO format for nested models
+        json_str = context_result.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["primary_result"]["created_at"] == "2023-12-08T09:30:15"
+        assert data["observations"][0]["created_at"] == "2023-12-08T09:30:15"
+
+    def test_graph_context_full_serialization(self):
+        """Test full GraphContext serialization with all datetime fields."""
+        test_datetime = datetime(2023, 12, 8, 14, 20, 10)
+        
+        entity = EntitySummary(
+            permalink="test/entity",
+            title="Test Entity",
+            file_path="test/entity.md",
+            created_at=test_datetime
+        )
+        
+        metadata = MemoryMetadata(
+            depth=1,
+            generated_at=test_datetime,
+            primary_count=1,
+            related_count=0
+        )
+        
+        context_result = ContextResult(
+            primary_result=entity,
+            observations=[],
+            related_results=[]
+        )
+        
+        graph_context = GraphContext(
+            results=[context_result],
+            metadata=metadata,
+            page=1,
+            page_size=10
+        )
+        
+        # Test full serialization
+        json_str = graph_context.model_dump_json()
+        data = json.loads(json_str)
+        
+        assert data["metadata"]["generated_at"] == "2023-12-08T14:20:10"
+        assert data["results"][0]["primary_result"]["created_at"] == "2023-12-08T14:20:10"
+
+    def test_datetime_with_microseconds_serialization(self):
+        """Test datetime with microseconds serializes correctly."""
+        test_datetime = datetime(2023, 12, 8, 10, 30, 0, 123456)
+        
+        entity = EntitySummary(
+            permalink="test/entity",
+            title="Test Entity",
+            file_path="test/entity.md",
+            created_at=test_datetime
+        )
+        
+        json_str = entity.model_dump_json()
+        data = json.loads(json_str)
+        
+        # Should include microseconds in ISO format
+        assert data["created_at"] == "2023-12-08T10:30:00.123456"
+
+    def test_mcp_schema_validation_compatibility(self):
+        """Test that serialized datetime format is compatible with MCP schema validation."""
+        test_datetime = datetime(2023, 12, 8, 10, 30, 0)
+        
+        entity = EntitySummary(
+            permalink="test/entity",
+            title="Test Entity", 
+            file_path="test/entity.md",
+            created_at=test_datetime
+        )
+        
+        # Serialize to JSON
+        json_str = entity.model_dump_json()
+        data = json.loads(json_str)
+        
+        # Verify the format matches expected MCP "date-time" format
+        datetime_str = data["created_at"]
+        
+        # Should be parseable back to datetime (ISO format validation)
+        parsed_datetime = datetime.fromisoformat(datetime_str)
+        assert parsed_datetime == test_datetime
+        
+        # Should match the expected ISO format pattern
+        assert "T" in datetime_str  # Contains date-time separator
+        assert len(datetime_str) >= 19  # At least YYYY-MM-DDTHH:MM:SS format
+
+    def test_all_models_have_json_encoders_configured(self):
+        """Test that all memory schema models have datetime json_encoders configured."""
+        models_to_test = [
+            EntitySummary,
+            RelationSummary, 
+            ObservationSummary,
+            MemoryMetadata
+        ]
+        
+        for model_class in models_to_test:
+            # Check that ConfigDict with json_encoders is configured
+            assert hasattr(model_class, 'model_config')
+            assert 'json_encoders' in model_class.model_config
+            assert datetime in model_class.model_config['json_encoders']
+            
+            # Verify the encoder function produces ISO format
+            encoder = model_class.model_config['json_encoders'][datetime]
+            test_datetime = datetime(2023, 12, 8, 10, 30, 0)
+            result = encoder(test_datetime)
+            assert result == "2023-12-08T10:30:00"

tests/schemas/test_schemas.py

@@ -315,20 +315,21 @@ class TestTimeframeParsing:
     """Test cases for parse_timeframe() and validate_timeframe() functions."""
 
     def test_parse_timeframe_today(self):
-        """Test that parse_timeframe('today') returns start of current day."""
+        """Test that parse_timeframe('today') returns start of current day with timezone."""
         result = parse_timeframe("today")
-        expected = datetime.combine(datetime.now().date(), time.min)
+        expected = datetime.combine(datetime.now().date(), time.min).astimezone()
 
         assert result == expected
         assert result.hour == 0
         assert result.minute == 0
         assert result.second == 0
         assert result.microsecond == 0
+        assert result.tzinfo is not None
 
     def test_parse_timeframe_today_case_insensitive(self):
         """Test that parse_timeframe handles 'today' case-insensitively."""
         test_cases = ["today", "TODAY", "Today", "ToDay"]
-        expected = datetime.combine(datetime.now().date(), time.min)
+        expected = datetime.combine(datetime.now().date(), time.min).astimezone()
 
         for case in test_cases:
             result = parse_timeframe(case)
@@ -336,24 +337,27 @@ class TestTimeframeParsing:
 
     def test_parse_timeframe_other_formats(self):
         """Test that parse_timeframe works with other dateparser formats."""
-        now = datetime.now()
+        now = datetime.now().astimezone()
 
         # Test 1d ago - should be approximately 24 hours ago
         result_1d = parse_timeframe("1d")
         expected_1d = now - timedelta(days=1)
         diff = abs((result_1d - expected_1d).total_seconds())
         assert diff < 60  # Within 1 minute tolerance
+        assert result_1d.tzinfo is not None
 
         # Test yesterday - should be yesterday at same time
         result_yesterday = parse_timeframe("yesterday")
         # dateparser returns yesterday at current time, not start of yesterday
         assert result_yesterday.date() == (now.date() - timedelta(days=1))
+        assert result_yesterday.tzinfo is not None
 
         # Test 1 week ago
         result_week = parse_timeframe("1 week ago")
         expected_week = now - timedelta(weeks=1)
         diff = abs((result_week - expected_week).total_seconds())
         assert diff < 3600  # Within 1 hour tolerance
+        assert result_week.tzinfo is not None
 
     def test_parse_timeframe_invalid(self):
         """Test that parse_timeframe raises ValueError for invalid input."""
@@ -448,7 +452,7 @@ class TestTimeframeParsing:
         assert today_parsed.minute == 0
 
         # '1d' should be 24 hours ago (same time yesterday)
-        now = datetime.now()
+        now = datetime.now().astimezone()
         expected_1d = now - timedelta(days=1)
         diff = abs((oneday_parsed - expected_1d).total_seconds())
         assert diff < 60  # Within 1 minute

tests/services/test_context_service.py

@@ -9,6 +9,8 @@ from basic_memory.repository.search_repository import SearchIndexRow
 from basic_memory.schemas.memory import memory_url, memory_url_path
 from basic_memory.schemas.search import SearchItemType
 from basic_memory.services.context_service import ContextService
+from basic_memory.models.knowledge import Entity, Relation
+from basic_memory.models.project import Project
 
 
 @pytest_asyncio.fixture
@@ -218,3 +220,101 @@ async def test_context_metadata(context_service, test_graph):
     assert metadata.depth == 2
     assert metadata.generated_at is not None
     assert metadata.primary_count > 0
+
+
+@pytest.mark.asyncio 
+async def test_project_isolation_in_find_related(session_maker):
+    """Test that find_related respects project boundaries and doesn't leak data."""
+    from basic_memory.repository.entity_repository import EntityRepository
+    from basic_memory.repository.observation_repository import ObservationRepository
+    from basic_memory.repository.search_repository import SearchRepository
+    from basic_memory import db
+    
+    # Create database session
+    async with db.scoped_session(session_maker) as db_session:
+        # Create two separate projects
+        project1 = Project(name="project1", path="/test1")
+        project2 = Project(name="project2", path="/test2")
+        db_session.add(project1)
+        db_session.add(project2)
+        await db_session.flush()
+        
+        # Create entities in project1
+        entity1_p1 = Entity(
+            title="Entity1_P1",
+            entity_type="document", 
+            content_type="text/markdown",
+            project_id=project1.id,
+            permalink="project1/entity1",
+            file_path="project1/entity1.md",
+            created_at=datetime.now(UTC),
+            updated_at=datetime.now(UTC)
+        )
+        entity2_p1 = Entity(
+            title="Entity2_P1", 
+            entity_type="document",
+            content_type="text/markdown", 
+            project_id=project1.id,
+            permalink="project1/entity2",
+            file_path="project1/entity2.md", 
+            created_at=datetime.now(UTC),
+            updated_at=datetime.now(UTC)
+        )
+        
+        # Create entities in project2
+        entity1_p2 = Entity(
+            title="Entity1_P2",
+            entity_type="document",
+            content_type="text/markdown",
+            project_id=project2.id, 
+            permalink="project2/entity1",
+            file_path="project2/entity1.md",
+            created_at=datetime.now(UTC),
+            updated_at=datetime.now(UTC)
+        )
+        
+        db_session.add_all([entity1_p1, entity2_p1, entity1_p2])
+        await db_session.flush()
+        
+        # Create relation in project1 (between entities of project1)
+        relation_p1 = Relation(
+            from_id=entity1_p1.id,
+            to_id=entity2_p1.id,
+            to_name="Entity2_P1",
+            relation_type="connects_to"
+        )
+        db_session.add(relation_p1)
+        await db_session.commit()
+        
+        # Create repositories for project1 
+        search_repo_p1 = SearchRepository(session_maker, project1.id)
+        entity_repo_p1 = EntityRepository(session_maker, project1.id)
+        obs_repo_p1 = ObservationRepository(session_maker, project1.id)
+        context_service_p1 = ContextService(search_repo_p1, entity_repo_p1, obs_repo_p1)
+        
+        # Create repositories for project2
+        search_repo_p2 = SearchRepository(session_maker, project2.id)
+        entity_repo_p2 = EntityRepository(session_maker, project2.id)  
+        obs_repo_p2 = ObservationRepository(session_maker, project2.id)
+        context_service_p2 = ContextService(search_repo_p2, entity_repo_p2, obs_repo_p2)
+        
+        # Test: find_related for project1 should only return project1 entities
+        type_id_pairs_p1 = [("entity", entity1_p1.id)]
+        related_p1 = await context_service_p1.find_related(type_id_pairs_p1, max_depth=2)
+        
+        # Verify only project1 entities are returned
+        related_entity_ids = [r.id for r in related_p1 if r.type == "entity"]
+        assert entity2_p1.id in related_entity_ids  # Should find connected entity2 in project1
+        assert entity1_p2.id not in related_entity_ids  # Should NOT find entity from project2
+        
+        # Test: find_related for project2 should return empty (no relations)
+        type_id_pairs_p2 = [("entity", entity1_p2.id)]
+        related_p2 = await context_service_p2.find_related(type_id_pairs_p2, max_depth=2)
+        
+        # Project2 has no relations, so should return empty
+        assert len(related_p2) == 0
+        
+        # Double-check: verify entities exist in their respective projects
+        assert entity1_p1.project_id == project1.id
+        assert entity2_p1.project_id == project1.id
+        assert entity1_p2.project_id == project2.id

tests/services/test_directory_service.py

@@ -168,6 +168,28 @@ async def test_list_directory_path_normalization(directory_service: DirectorySer
         assert result_names == base_names
 
 
+@pytest.mark.asyncio
+async def test_list_directory_dot_slash_prefix_normalization(
+    directory_service: DirectoryService, test_graph
+):
+    """Test that ./ prefixed directory paths are normalized correctly."""
+    # This test reproduces the bug report issue where ./dirname fails
+    base_result = await directory_service.list_directory(dir_name="/test")
+
+    # Test paths with ./ prefix that should be equivalent to /test
+    dot_paths_to_test = ["./test", "./test/"]
+
+    for path in dot_paths_to_test:
+        result = await directory_service.list_directory(dir_name=path)
+        assert len(result) == len(base_result), (
+            f"Path '{path}' returned {len(result)} results, expected {len(base_result)}"
+        )
+        # Compare by name since the objects might be different instances
+        result_names = {node.name for node in result}
+        base_names = {node.name for node in base_result}
+        assert result_names == base_names, f"Path '{path}' returned different files than expected"
+
+
 @pytest.mark.asyncio
 async def test_list_directory_glob_no_matches(directory_service: DirectoryService, test_graph):
     """Test listing directory with glob that matches nothing."""

tests/services/test_entity_service.py

@@ -592,7 +592,7 @@ async def test_create_with_no_frontmatter(
     created = await entity_service.create_entity_from_markdown(file_path, entity_markdown)
     file_content, _ = await file_service.read_file(created.file_path)
 
-    assert str(file_path) == str(created.file_path)
+    assert file_path.as_posix() == created.file_path
     assert created.title == "Git Workflow Guide"
     assert created.entity_type == "note"
     assert created.permalink is None
@@ -898,7 +898,7 @@ async def test_create_entity_from_markdown_with_upsert(
     # Verify it created the entity successfully using the UPSERT approach
     assert result is not None
     assert result.title == "UPSERT Test"
-    assert result.file_path == str(file_path)
+    assert result.file_path == file_path.as_posix()
     # create_entity_from_markdown sets checksum to None (incomplete sync)
     assert result.checksum is None
 

tests/services/test_project_removal_bug.py

@@ -0,0 +1,125 @@
+"""Test for project removal bug #254."""
+
+import os
+from datetime import timezone, datetime
+
+import pytest
+
+from basic_memory.services.project_service import ProjectService
+
+
+@pytest.mark.asyncio
+async def test_remove_project_with_related_entities(project_service: ProjectService, tmp_path):
+    """Test removing a project that has related entities (reproduces issue #254).
+    
+    This test verifies that projects with related entities (entities, observations, relations)
+    can be properly deleted without foreign key constraint violations.
+    
+    The bug was caused by missing foreign key constraints with CASCADE DELETE after
+    the project table was recreated in migration 647e7a75e2cd.
+    """
+    test_project_name = f"test-remove-with-entities-{os.urandom(4).hex()}"
+    test_project_path = str(tmp_path / "test-remove-with-entities")
+
+    # Make sure the test directory exists
+    os.makedirs(test_project_path, exist_ok=True)
+
+    try:
+        # Step 1: Add the test project
+        await project_service.add_project(test_project_name, test_project_path)
+        
+        # Verify project exists
+        project = await project_service.get_project(test_project_name)
+        assert project is not None
+        
+        # Step 2: Create related entities for this project
+        from basic_memory.repository.entity_repository import EntityRepository
+        entity_repo = EntityRepository(project_service.repository.session_maker, project_id=project.id)
+        
+        entity_data = {
+            "title": "Test Entity for Deletion",
+            "entity_type": "note", 
+            "content_type": "text/markdown",
+            "project_id": project.id,
+            "permalink": "test-deletion-entity",
+            "file_path": "test-deletion-entity.md",
+            "checksum": "test123",
+            "created_at": datetime.now(timezone.utc),
+            "updated_at": datetime.now(timezone.utc),
+        }
+        entity = await entity_repo.create(entity_data)
+        assert entity is not None
+        
+        # Step 3: Create observations for the entity
+        from basic_memory.repository.observation_repository import ObservationRepository
+        obs_repo = ObservationRepository(project_service.repository.session_maker, project_id=project.id)
+        
+        observation_data = {
+            "entity_id": entity.id,
+            "content": "This is a test observation",
+            "category": "note"
+        }
+        observation = await obs_repo.create(observation_data)
+        assert observation is not None
+        
+        # Step 4: Create relations involving the entity 
+        from basic_memory.repository.relation_repository import RelationRepository
+        rel_repo = RelationRepository(project_service.repository.session_maker, project_id=project.id)
+        
+        relation_data = {
+            "from_id": entity.id,
+            "to_name": "some-target-entity",
+            "relation_type": "relates-to"
+        }
+        relation = await rel_repo.create(relation_data)
+        assert relation is not None
+        
+        # Step 5: Attempt to remove the project
+        # This should work with proper cascade delete, or fail with foreign key constraint
+        await project_service.remove_project(test_project_name)
+        
+        # Step 6: Verify everything was properly deleted
+        
+        # Project should be gone
+        removed_project = await project_service.get_project(test_project_name)
+        assert removed_project is None, "Project should have been removed"
+        
+        # Related entities should be cascade deleted
+        remaining_entity = await entity_repo.find_by_id(entity.id)
+        assert remaining_entity is None, "Entity should have been cascade deleted"
+        
+        # Observations should be cascade deleted
+        remaining_obs = await obs_repo.find_by_id(observation.id)
+        assert remaining_obs is None, "Observation should have been cascade deleted"
+        
+        # Relations should be cascade deleted  
+        remaining_rel = await rel_repo.find_by_id(relation.id)
+        assert remaining_rel is None, "Relation should have been cascade deleted"
+        
+    except Exception as e:
+        # Check if this is the specific foreign key constraint error from the bug report
+        if "FOREIGN KEY constraint failed" in str(e):
+            pytest.fail(
+                f"Bug #254 reproduced: {e}. "
+                "This indicates missing foreign key constraints with CASCADE DELETE. "
+                "Run migration a1b2c3d4e5f6_fix_project_foreign_keys.py to fix this."
+            )
+        else:
+            # Re-raise other unexpected errors
+            raise e
+    
+    finally:
+        # Clean up - remove project if it still exists
+        if test_project_name in project_service.projects:
+            try:
+                await project_service.remove_project(test_project_name)
+            except Exception:
+                # Manual cleanup if remove_project fails
+                try:
+                    project_service.config_manager.remove_project(test_project_name)
+                except Exception:
+                    pass
+                
+                project = await project_service.get_project(test_project_name)
+                if project:
+                    await project_service.repository.delete(project.id)

tests/services/test_project_service.py

@@ -1,6 +1,7 @@
 """Tests for ProjectService."""
 
 import os
+from pathlib import Path
 
 import pytest
 
@@ -73,7 +74,7 @@ async def test_project_operations_sync_methods(
     """
     # Generate a unique project name for testing
     test_project_name = f"test-project-{os.urandom(4).hex()}"
-    test_project_path = str(tmp_path / "test-project")
+    test_project_path = (tmp_path / "test-project").as_posix()
 
     # Make sure the test directory exists
     os.makedirs(test_project_path, exist_ok=True)
@@ -167,7 +168,7 @@ async def test_get_project_info(project_service: ProjectService, test_graph, tes
 async def test_add_project_async(project_service: ProjectService, tmp_path):
     """Test adding a project with the updated async method."""
     test_project_name = f"test-async-project-{os.urandom(4).hex()}"
-    test_project_path = str(tmp_path / "test-async-project")
+    test_project_path = (tmp_path / "test-async-project").as_posix()
 
     # Make sure the test directory exists
     os.makedirs(test_project_path, exist_ok=True)
@@ -243,7 +244,7 @@ async def test_set_default_project_async(project_service: ProjectService, tmp_pa
 async def test_get_project_method(project_service: ProjectService, tmp_path):
     """Test the get_project method directly."""
     test_project_name = f"test-get-project-{os.urandom(4).hex()}"
-    test_project_path = str(tmp_path / "test-get-project")
+    test_project_path = (tmp_path / "test-get-project").as_posix()
 
     # Make sure the test directory exists
     os.makedirs(test_project_path, exist_ok=True)
@@ -539,8 +540,8 @@ async def test_synchronize_projects_normalizes_project_names(
 async def test_move_project(project_service: ProjectService, tmp_path):
     """Test moving a project to a new location."""
     test_project_name = f"test-move-project-{os.urandom(4).hex()}"
-    old_path = str(tmp_path / "old-location")
-    new_path = str(tmp_path / "new-location")
+    old_path = (tmp_path / "old-location").as_posix()
+    new_path = (tmp_path / "new-location").as_posix()
 
     # Create old directory
     os.makedirs(old_path, exist_ok=True)
@@ -590,8 +591,8 @@ async def test_move_project_nonexistent(project_service: ProjectService, tmp_pat
 async def test_move_project_db_mismatch(project_service: ProjectService, tmp_path):
     """Test moving a project that exists in config but not in database."""
     test_project_name = f"test-move-mismatch-{os.urandom(4).hex()}"
-    old_path = str(tmp_path / "old-location")
-    new_path = str(tmp_path / "new-location")
+    old_path = (tmp_path / "old-location").as_posix()
+    new_path = (tmp_path / "new-location").as_posix()
 
     # Create directories
     os.makedirs(old_path, exist_ok=True)
@@ -624,7 +625,7 @@ async def test_move_project_db_mismatch(project_service: ProjectService, tmp_pat
 async def test_move_project_expands_path(project_service: ProjectService, tmp_path):
     """Test that move_project expands ~ and relative paths."""
     test_project_name = f"test-move-expand-{os.urandom(4).hex()}"
-    old_path = str(tmp_path / "old-location")
+    old_path = (tmp_path / "old-location").as_posix()
 
     # Create old directory
     os.makedirs(old_path, exist_ok=True)
@@ -635,7 +636,7 @@ async def test_move_project_expands_path(project_service: ProjectService, tmp_pa
 
         # Use a relative path for the move
         relative_new_path = "./new-location"
-        expected_absolute_path = os.path.abspath(relative_new_path)
+        expected_absolute_path = Path(os.path.abspath(relative_new_path)).as_posix()
 
         # Move project using relative path
         await project_service.move_project(test_project_name, relative_new_path)
@@ -712,4 +713,4 @@ async def test_synchronize_projects_handles_case_sensitivity_bug(
 
                     db_project = await project_service.repository.get_by_name(name)
                     if db_project:
-                        await project_service.repository.delete(db_project.id)
+                        await project_service.repository.delete(db_project.id)

tests/services/test_project_service_operations.py

@@ -48,7 +48,7 @@ async def test_add_project_to_config(project_service: ProjectService, tmp_path,
     """Test adding a project to the config manager."""
     # Generate unique project name for testing
     test_project_name = f"config-project-{os.urandom(4).hex()}"
-    test_path = str(tmp_path / "config-project")
+    test_path = (tmp_path / "config-project").as_posix()
 
     # Make sure directory exists
     os.makedirs(test_path, exist_ok=True)
@@ -72,8 +72,8 @@ async def test_update_project_path(project_service: ProjectService, tmp_path, co
     """Test updating a project's path."""
     # Create a test project
     test_project = f"path-update-test-project-{os.urandom(4).hex()}"
-    original_path = str(tmp_path / "original-path")
-    new_path = str(tmp_path / "new-path")
+    original_path = (tmp_path / "original-path").as_posix()
+    new_path = (tmp_path / "new-path").as_posix()
 
     # Make sure directories exist
     os.makedirs(original_path, exist_ok=True)

tests/services/test_search_service.py

@@ -155,7 +155,7 @@ async def test_after_date(search_service, test_graph):
     """Test search filters."""
 
     # Should find with past date
-    past_date = datetime(2020, 1, 1)
+    past_date = datetime(2020, 1, 1).astimezone()
     results = await search_service.search(
         SearchQuery(
             text="entity",
@@ -166,7 +166,7 @@ async def test_after_date(search_service, test_graph):
         assert datetime.fromisoformat(r.created_at) > past_date
 
     # Should not find with future date
-    future_date = datetime(2030, 1, 1)
+    future_date = datetime(2030, 1, 1).astimezone()
     results = await search_service.search(
         SearchQuery(
             text="entity",

tests/sync/test_character_conflicts.py

@@ -225,7 +225,7 @@ class TestSyncConflictHandling:
     ):
         """Test conflict handling when case differences cause issues."""
         import platform
-        
+
         project_dir = project_config.home
 
         # Create directory structure that might cause case conflicts
@@ -256,7 +256,7 @@ class TestSyncConflictHandling:
 
         # Verify entities were created
         entities = await entity_repository.find_all()
-        
+
         # On case-insensitive file systems (macOS, Windows), only one entity will be created
         # On case-sensitive file systems (Linux), two entities will be created
         if platform.system() in ["Darwin", "Windows"]:
@@ -264,7 +264,9 @@ class TestSyncConflictHandling:
             assert len(entities) >= 1
             # Only one of the paths will exist
             file_paths = [entity.file_path for entity in entities]
-            assert any(path in ["Finance/investment.md", "finance/investment.md"] for path in file_paths)
+            assert any(
+                path in ["Finance/investment.md", "finance/investment.md"] for path in file_paths
+            )
         else:
             # Case-sensitive file systems (Linux)
             assert len(entities) >= 2

tests/sync/test_sync_service.py

@@ -617,7 +617,7 @@ type: knowledge
 # File Dates
 Testing file timestamps
 """
-    file_path = project_dir / "file_dates.md"
+    file_path = project_dir / "file_dates3.md"
     await create_test_file(file_path, file_dates_content)
 
     # Run sync
@@ -629,13 +629,19 @@ Testing file timestamps
     assert explicit_entity.updated_at is not None
 
     # Check file timestamps
-    file_entity = await entity_service.get_by_permalink("file-dates")
+    file_entity = await entity_service.get_by_permalink("file-dates3")
     file_stats = file_path.stat()
+    
+    # Compare using epoch timestamps to handle timezone differences correctly
+    # This ensures we're comparing the actual points in time, not display representations
+    entity_created_epoch = file_entity.created_at.timestamp()
+    entity_updated_epoch = file_entity.updated_at.timestamp()
+    
     assert (
-        abs((file_entity.created_at.timestamp() - file_stats.st_ctime)) < 1
-    )  # Allow 1s difference
+        abs(entity_created_epoch - file_stats.st_ctime) < 1
+    )
     assert (
-        abs((file_entity.updated_at.timestamp() - file_stats.st_mtime)) < 1
+        abs(entity_updated_epoch - file_stats.st_mtime) < 1
     )  # Allow 1s difference
 
 
@@ -674,7 +680,7 @@ Content for move test
     # Check search index has updated path
     results = await search_service.search(SearchQuery(text="Content for move test"))
     assert len(results) == 1
-    assert results[0].file_path == str(new_path.relative_to(project_dir))
+    assert results[0].file_path == new_path.relative_to(project_dir).as_posix()
 
 
 @pytest.mark.asyncio

tests/sync/test_tmp_files.py

@@ -122,7 +122,7 @@ async def test_rapid_atomic_writes(watch_service, project_config, test_project,
     await create_test_file(tmp2_path, "Second version")
 
     # Simulate the first atomic write
-    tmp1_path.rename(final_path)
+    tmp1_path.replace(final_path)
 
     # Brief pause to ensure file system registers the change
     await asyncio.sleep(0.1)
@@ -132,7 +132,7 @@ async def test_rapid_atomic_writes(watch_service, project_config, test_project,
     assert content1 == "First version"
 
     # Simulate the second atomic write
-    tmp2_path.rename(final_path)
+    tmp2_path.replace(final_path)
 
     # Verify content was updated
     content2 = final_path.read_text(encoding="utf-8")

tests/sync/test_watch_service_edge_cases.py

@@ -66,3 +66,208 @@ async def test_handle_changes_empty_set(watch_service, project_config, test_proj
 
             # Verify synced_files wasn't changed
             assert watch_service.state.synced_files == 0
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_delete_still_exists(watch_service, project_config, test_project, sync_service):
+    """Test vim atomic write scenario: DELETE event but file still exists on disk."""
+    project_dir = project_config.home
+
+    # Create initial file and sync it
+    test_file = project_dir / "vim_test.md"
+    initial_content = """---
+type: note
+title: vim test
+---
+# Vim Test
+Initial content for atomic write test
+"""
+    test_file.write_text(initial_content)
+    await sync_service.sync(project_dir)
+    
+    # Get initial entity state
+    initial_entity = await sync_service.entity_repository.get_by_file_path("vim_test.md")
+    assert initial_entity is not None
+    initial_checksum = initial_entity.checksum
+
+    # Simulate vim's atomic write: modify content but send DELETE event
+    # (vim moves original file, creates new content, then deletes old inode)
+    modified_content = """---
+type: note
+title: vim test
+---
+# Vim Test
+Modified content after atomic write
+"""
+    test_file.write_text(modified_content)
+
+    # Setup DELETE event even though file still exists (vim's atomic write behavior)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(test_file))}
+
+    # Handle the change
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify the entity still exists and was updated (not deleted)
+    entity = await sync_service.entity_repository.get_by_file_path("vim_test.md")
+    assert entity is not None
+    assert entity.id == initial_entity.id  # Same entity
+    assert entity.checksum != initial_checksum  # Checksum should be updated
+
+    # Verify the file content was properly synced
+    actual_content = test_file.read_text()
+    assert "Modified content after atomic write" in actual_content
+
+    # Check that correct event was recorded (should be "modified", not "deleted")
+    events = [e for e in watch_service.state.recent_events if e.path == "vim_test.md"]
+    assert len(events) == 1
+    assert events[0].action == "modified"
+    assert events[0].status == "success"
+
+
+@pytest.mark.asyncio
+async def test_handle_true_deletion_vs_vim_atomic(watch_service, project_config, test_project, sync_service):
+    """Test that true deletions are still handled correctly vs vim atomic writes."""
+    project_dir = project_config.home
+
+    # Create and sync two files
+    atomic_file = project_dir / "atomic_test.md"
+    delete_file = project_dir / "delete_test.md"
+    
+    content = """---
+type: note
+---
+# Test File
+Content for testing
+"""
+    
+    atomic_file.write_text(content)
+    delete_file.write_text(content)
+    await sync_service.sync(project_dir)
+
+    # For atomic_file: modify content but keep file (vim atomic write scenario)
+    modified_content = content.replace("Content for testing", "Modified content")
+    atomic_file.write_text(modified_content)
+
+    # For delete_file: actually delete it (true deletion)
+    delete_file.unlink()
+
+    # Setup DELETE events for both files
+    # Use absolute paths like the real watch service would
+    changes = {
+        (Change.deleted, str(atomic_file)),  # File still exists - atomic write
+        (Change.deleted, str(delete_file)),  # File deleted - true deletion
+    }
+
+    # Handle the changes
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify atomic_file was treated as modification (still exists in DB)
+    atomic_entity = await sync_service.entity_repository.get_by_file_path("atomic_test.md")
+    assert atomic_entity is not None
+
+    # Verify delete_file was truly deleted (no longer exists in DB)
+    delete_entity = await sync_service.entity_repository.get_by_file_path("delete_test.md")
+    assert delete_entity is None
+
+    # Check events were recorded correctly
+    events = watch_service.state.recent_events
+    atomic_events = [e for e in events if e.path == "atomic_test.md"]
+    delete_events = [e for e in events if e.path == "delete_test.md"]
+    
+    assert len(atomic_events) == 1
+    assert atomic_events[0].action == "modified"
+    
+    assert len(delete_events) == 1
+    assert delete_events[0].action == "deleted"
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_markdown_with_relations(watch_service, project_config, test_project, sync_service):
+    """Test vim atomic write with markdown files that contain relations."""
+    project_dir = project_config.home
+
+    # Create target file for relations
+    target_file = project_dir / "target.md"
+    target_content = """---
+type: note
+title: Target Note
+---
+# Target Note
+This is the target of relations.
+"""
+    target_file.write_text(target_content)
+
+    # Create main file with relations
+    main_file = project_dir / "main.md"
+    initial_content = """---
+type: note
+title: Main Note
+---
+# Main Note
+This note links to [[Target Note]].
+
+- relates_to [[Target Note]]
+"""
+    main_file.write_text(initial_content)
+    await sync_service.sync(project_dir)
+
+    # Get initial state
+    main_entity = await sync_service.entity_repository.get_by_file_path("main.md")
+    assert main_entity is not None
+    initial_relations = len(main_entity.relations)
+
+    # Simulate vim atomic write with content change that adds more relations
+    modified_content = """---
+type: note
+title: Main Note
+---
+# Main Note
+This note links to [[Target Note]] multiple times.
+
+- relates_to [[Target Note]]
+- references [[Target Note]]
+"""
+    main_file.write_text(modified_content)
+
+    # Setup DELETE event (vim atomic write)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(main_file))}
+
+    # Handle the change
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify entity still exists and relations were updated
+    updated_entity = await sync_service.entity_repository.get_by_file_path("main.md")
+    assert updated_entity is not None
+    assert updated_entity.id == main_entity.id
+    
+    # Verify relations were processed correctly
+    updated_relations = len(updated_entity.relations)
+    assert updated_relations >= initial_relations  # Should have at least as many relations
+
+    # Check event was recorded as modification
+    events = [e for e in watch_service.state.recent_events if e.path == "main.md"]
+    assert len(events) == 1
+    assert events[0].action == "modified"
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_directory_path_ignored(watch_service, project_config, test_project):
+    """Test that directories are properly ignored even in atomic write detection."""
+    project_dir = project_config.home
+
+    # Create directory
+    test_dir = project_dir / "test_directory"
+    test_dir.mkdir()
+
+    # Setup DELETE event for directory (should be ignored)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(test_dir))}
+
+    # Handle the change - should not cause errors
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify no events were recorded for the directory
+    events = [e for e in watch_service.state.recent_events if "test_directory" in e.path]
+    assert len(events) == 0

tests/test_config.py

@@ -1,7 +1,10 @@
 """Test configuration management."""
 
-from basic_memory.config import BasicMemoryConfig
+import tempfile
+import pytest
 
+from basic_memory.config import BasicMemoryConfig, ConfigManager
+from pathlib import Path
 
 class TestBasicMemoryConfig:
     """Test BasicMemoryConfig behavior with BASIC_MEMORY_HOME environment variable."""
@@ -14,12 +17,12 @@ class TestBasicMemoryConfig:
         config = BasicMemoryConfig()
 
         # Should use the default path (home/basic-memory)
-        expected_path = str(config_home / "basic-memory")
-        assert config.projects["main"] == expected_path
+        expected_path = (config_home / "basic-memory").as_posix()
+        assert config.projects["main"] == Path(expected_path).as_posix()
 
     def test_respects_basic_memory_home_environment_variable(self, config_home, monkeypatch):
         """Test that config respects BASIC_MEMORY_HOME environment variable."""
-        custom_path = str(config_home / "app" / "data")
+        custom_path = (config_home / "app" / "data").as_posix()
         monkeypatch.setenv("BASIC_MEMORY_HOME", custom_path)
 
         config = BasicMemoryConfig()
@@ -38,7 +41,7 @@ class TestBasicMemoryConfig:
 
         # model_post_init should have added main project with BASIC_MEMORY_HOME
         assert "main" in config.projects
-        assert config.projects["main"] == custom_path
+        assert config.projects["main"] == Path(custom_path).as_posix()
 
     def test_model_post_init_fallback_without_basic_memory_home(self, config_home, monkeypatch):
         """Test that model_post_init falls back to default when BASIC_MEMORY_HOME is not set."""
@@ -46,13 +49,13 @@ class TestBasicMemoryConfig:
         monkeypatch.delenv("BASIC_MEMORY_HOME", raising=False)
 
         # Create config without main project
-        other_path = str(config_home / "some" / "path")
+        other_path = (config_home / "some" / "path").as_posix()
         config = BasicMemoryConfig(projects={"other": other_path})
 
         # model_post_init should have added main project with default path
-        expected_path = str(config_home / "basic-memory")
+        expected_path = (config_home / "basic-memory").as_posix()
         assert "main" in config.projects
-        assert config.projects["main"] == expected_path
+        assert config.projects["main"] == Path(expected_path).as_posix()
 
     def test_basic_memory_home_with_relative_path(self, config_home, monkeypatch):
         """Test that BASIC_MEMORY_HOME works with relative paths."""
@@ -76,3 +79,88 @@ class TestBasicMemoryConfig:
         # The default_factory should override with BASIC_MEMORY_HOME value
         # Note: This tests the current behavior where default_factory takes precedence
         assert config.projects["main"] == original_path
+
+
+class TestConfigManager:
+    """Test ConfigManager functionality."""
+    
+    @pytest.fixture
+    def temp_config_manager(self):
+        """Create a ConfigManager with temporary config file."""
+        with tempfile.TemporaryDirectory() as temp_dir:
+            temp_path = Path(temp_dir)
+            
+            # Create a test ConfigManager instance
+            config_manager = ConfigManager()
+            # Override config paths to use temp directory
+            config_manager.config_dir = temp_path / "basic-memory"
+            config_manager.config_file = config_manager.config_dir / "config.yaml"
+            config_manager.config_dir.mkdir(parents=True, exist_ok=True)
+            
+            # Create initial config with test projects
+            test_config = BasicMemoryConfig(
+                default_project="main",
+                projects={
+                    "main": str(temp_path / "main"),
+                    "test-project": str(temp_path / "test"),
+                    "special-chars": str(temp_path / "special")  # This will be the config key for "Special/Chars"
+                }
+            )
+            config_manager.save_config(test_config)
+            
+            yield config_manager
+    
+    def test_set_default_project_with_exact_name_match(self, temp_config_manager):
+        """Test set_default_project when project name matches config key exactly."""
+        config_manager = temp_config_manager
+        
+        # Set default to a project that exists with exact name match
+        config_manager.set_default_project("test-project")
+        
+        # Verify the config was updated
+        config = config_manager.load_config()
+        assert config.default_project == "test-project"
+    
+    def test_set_default_project_with_permalink_lookup(self, temp_config_manager):
+        """Test set_default_project when input needs permalink normalization."""
+        config_manager = temp_config_manager
+        
+        # Simulate a project that was created with special characters
+        # The config key would be the permalink, but user might type the original name
+        
+        # First add a project with original name that gets normalized
+        config = config_manager.load_config()
+        config.projects["special-chars-project"] = str(Path("/tmp/special"))
+        config_manager.save_config(config)
+        
+        # Now test setting default using a name that will normalize to the config key
+        config_manager.set_default_project("Special Chars Project")  # This should normalize to "special-chars-project"
+        
+        # Verify the config was updated with the correct config key
+        updated_config = config_manager.load_config()
+        assert updated_config.default_project == "special-chars-project"
+    
+    def test_set_default_project_uses_canonical_name(self, temp_config_manager):
+        """Test that set_default_project uses the canonical config key, not user input."""
+        config_manager = temp_config_manager
+        
+        # Add a project with a config key that differs from user input
+        config = config_manager.load_config()
+        config.projects["my-test-project"] = str(Path("/tmp/mytest"))
+        config_manager.save_config(config)
+        
+        # Set default using input that will match but is different from config key
+        config_manager.set_default_project("My Test Project")  # Should find "my-test-project"
+        
+        # Verify that the canonical config key is used, not the user input
+        updated_config = config_manager.load_config()
+        assert updated_config.default_project == "my-test-project"
+        # Should NOT be the user input
+        assert updated_config.default_project != "My Test Project"
+    
+    def test_set_default_project_nonexistent_project(self, temp_config_manager):
+        """Test set_default_project raises ValueError for nonexistent project."""
+        config_manager = temp_config_manager
+        
+        with pytest.raises(ValueError, match="Project 'nonexistent' not found"):
+            config_manager.set_default_project("nonexistent")

tests/test_production_cascade_delete.py

@@ -0,0 +1,325 @@
+#!/usr/bin/env python3
+"""
+Test script to verify cascade delete behavior on production SQLite database.
+
+This script tests whether foreign key constraints with CASCADE DELETE are properly
+configured in the production database at ~/.basic-memory/memory.db.
+
+Usage: python test_production_cascade_delete.py
+"""
+
+import asyncio
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import Optional
+
+from sqlalchemy import text
+from sqlalchemy.ext.asyncio import create_async_engine, async_sessionmaker
+
+
+class ProductionCascadeTest:
+    """Test cascade delete behavior on production database."""
+    
+    def __init__(self, db_path: Optional[Path] = None):
+        """Initialize test with database path."""
+        if db_path is None:
+            # Default to standard Basic Memory location
+            home_dir = Path.home()
+            self.db_path = home_dir / ".basic-memory" / "memory.db"
+        else:
+            self.db_path = db_path
+            
+        # Create backup path
+        self.backup_path = self.db_path.with_suffix('.db.backup')
+        
+        self.engine = None
+        self.session_maker = None
+        
+    async def setup(self):
+        """Setup database connection."""
+        if not self.db_path.exists():
+            print(f"❌ Production database not found at: {self.db_path}")
+            print("Please ensure Basic Memory has been initialized and the database exists.")
+            sys.exit(1)
+            
+        print(f"📁 Using database: {self.db_path}")
+        
+        # Create backup
+        print(f"💾 Creating backup: {self.backup_path}")
+        import shutil
+        shutil.copy2(self.db_path, self.backup_path)
+        
+        # Connect to database
+        db_url = f"sqlite+aiosqlite:///{self.db_path}"
+        self.engine = create_async_engine(db_url, connect_args={"check_same_thread": False})
+        self.session_maker = async_sessionmaker(self.engine, expire_on_commit=False)
+        
+    async def cleanup(self):
+        """Cleanup database connection."""
+        if self.engine:
+            await self.engine.dispose()
+            
+    async def check_foreign_keys_enabled(self) -> bool:
+        """Check if foreign keys are enabled in this session."""
+        async with self.session_maker() as session:
+            # Enable foreign keys like production does
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+            
+            result = await session.execute(text("PRAGMA foreign_keys"))
+            fk_enabled = result.fetchone()[0]
+            return bool(fk_enabled)
+    
+    async def check_schema(self):
+        """Check current database schema for foreign key constraints."""
+        async with self.session_maker() as session:
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+            
+            # Check entity table foreign keys
+            result = await session.execute(text("PRAGMA foreign_key_list(entity)"))
+            entity_fks = result.fetchall()
+            
+            print("🔍 Current entity table foreign key constraints:")
+            for fk in entity_fks:
+                print(f"  - Column: {fk[3]} -> {fk[2]}.{fk[4]} (ON DELETE: {fk[6]})")
+                
+            # Check if CASCADE DELETE is configured
+            has_cascade = any(fk[6] == 'CASCADE' for fk in entity_fks)
+            
+            if has_cascade:
+                print("✅ CASCADE DELETE is configured")
+            else:
+                print("❌ CASCADE DELETE is NOT configured (uses NO ACTION)")
+                
+            return has_cascade
+    
+    async def create_test_data(self) -> tuple[int, int]:
+        """Create test project and entity. Returns (project_id, entity_id)."""
+        async with self.session_maker() as session:
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+            
+            # Create test project
+            project_sql = """
+            INSERT INTO project (name, description, permalink, path, is_active, is_default, created_at, updated_at)
+            VALUES (:name, :description, :permalink, :path, :is_active, :is_default, :created_at, :updated_at)
+            """
+            now = datetime.now(timezone.utc)
+            
+            result = await session.execute(text(project_sql), {
+                "name": "cascade-test-project",
+                "description": "Test project for cascade delete verification", 
+                "permalink": "cascade-test-project",
+                "path": "/tmp/cascade-test",
+                "is_active": True,
+                "is_default": False,
+                "created_at": now,
+                "updated_at": now
+            })
+            project_id = result.lastrowid
+            
+            # Create test entity linked to project
+            entity_sql = """
+            INSERT INTO entity (title, entity_type, content_type, project_id, permalink, file_path, 
+                              checksum, created_at, updated_at)
+            VALUES (:title, :entity_type, :content_type, :project_id, :permalink, :file_path, 
+                    :checksum, :created_at, :updated_at)
+            """
+            
+            result = await session.execute(text(entity_sql), {
+                "title": "Cascade Test Entity",
+                "entity_type": "note",
+                "content_type": "text/markdown", 
+                "project_id": project_id,
+                "permalink": "cascade-test-entity",
+                "file_path": "cascade-test-entity.md",
+                "checksum": "test-checksum",
+                "created_at": now,
+                "updated_at": now
+            })
+            entity_id = result.lastrowid
+            
+            await session.commit()
+            
+            print(f"📝 Created test project (ID: {project_id}) and entity (ID: {entity_id})")
+            return project_id, entity_id
+    
+    async def verify_test_data_exists(self, project_id: int, entity_id: int) -> bool:
+        """Verify test data exists before deletion."""
+        async with self.session_maker() as session:
+            # Check project exists
+            result = await session.execute(
+                text("SELECT COUNT(*) FROM project WHERE id = :project_id"), {"project_id": project_id}
+            )
+            project_count = result.fetchone()[0]
+            
+            # Check entity exists
+            result = await session.execute(
+                text("SELECT COUNT(*) FROM entity WHERE id = :entity_id"), {"entity_id": entity_id}
+            )
+            entity_count = result.fetchone()[0]
+            
+            exists = project_count > 0 and entity_count > 0
+            if exists:
+                print(f"✅ Test data verified: project ({project_count}) and entity ({entity_count}) exist")
+            else:
+                print(f"❌ Test data missing: project ({project_count}) and entity ({entity_count})")
+                
+            return exists
+    
+    async def test_cascade_delete(self, project_id: int, entity_id: int) -> bool:
+        """Test if deleting project cascades to delete entity."""
+        async with self.session_maker() as session:
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+            
+            try:
+                # Attempt to delete project
+                print(f"🗑️  Attempting to delete project (ID: {project_id})...")
+                
+                result = await session.execute(
+                    text("DELETE FROM project WHERE id = :project_id"), {"project_id": project_id}
+                )
+                
+                if result.rowcount == 0:
+                    print("❌ Project deletion failed - no rows affected")
+                    return False
+                    
+                await session.commit()
+                print("✅ Project deletion succeeded")
+                
+                # Check if entity was cascade deleted
+                result = await session.execute(
+                    text("SELECT COUNT(*) FROM entity WHERE id = :entity_id"), {"entity_id": entity_id}
+                )
+                entity_count = result.fetchone()[0]
+                
+                if entity_count == 0:
+                    print("✅ CASCADE DELETE working: Entity was automatically deleted")
+                    return True
+                else:
+                    print("❌ CASCADE DELETE NOT working: Entity still exists after project deletion")
+                    return False
+                    
+            except Exception as e:
+                await session.rollback()
+                print(f"❌ Project deletion failed with error: {e}")
+                
+                # Check if it's a foreign key constraint error
+                if "FOREIGN KEY constraint failed" in str(e):
+                    print("🔍 This confirms foreign key constraints are enforced but CASCADE DELETE is not configured")
+                
+                return False
+    
+    async def cleanup_test_data(self, project_id: int, entity_id: int):
+        """Clean up any remaining test data."""
+        async with self.session_maker() as session:
+            await session.execute(text("PRAGMA foreign_keys=ON"))
+            
+            try:
+                # Delete entity first (in case cascade didn't work)
+                await session.execute(text("DELETE FROM entity WHERE id = :entity_id"), {"entity_id": entity_id})
+                
+                # Delete project
+                await session.execute(text("DELETE FROM project WHERE id = :project_id"), {"project_id": project_id})
+                
+                await session.commit()
+                print("🧹 Cleaned up any remaining test data")
+                
+            except Exception as e:
+                print(f"⚠️  Error during cleanup: {e}")
+                await session.rollback()
+    
+    async def restore_backup(self):
+        """Restore database from backup."""
+        if self.backup_path.exists():
+            print("🔄 Restoring database from backup...")
+            import shutil
+            shutil.copy2(self.backup_path, self.db_path)
+            print("✅ Database restored from backup")
+            
+            # Remove backup file
+            self.backup_path.unlink()
+            print("🗑️  Backup file removed")
+        else:
+            print("⚠️  No backup file found to restore")
+    
+    async def run_test(self) -> bool:
+        """Run the complete cascade delete test."""
+        print("🧪 Production Database CASCADE DELETE Test")
+        print("=" * 50)
+        
+        try:
+            await self.setup()
+            
+            # Check if foreign keys are enabled
+            fk_enabled = await self.check_foreign_keys_enabled()
+            print(f"🔐 Foreign keys enabled: {fk_enabled}")
+            
+            if not fk_enabled:
+                print("❌ Foreign keys are not enabled - this test requires foreign key enforcement")
+                return False
+            
+            # Check current schema
+            has_cascade = await self.check_schema()
+            
+            # Create test data
+            project_id, entity_id = await self.create_test_data()
+            
+            # Verify test data exists
+            if not await self.verify_test_data_exists(project_id, entity_id):
+                return False
+            
+            # Test cascade delete
+            cascade_works = await self.test_cascade_delete(project_id, entity_id)
+            
+            # Clean up any remaining test data
+            await self.cleanup_test_data(project_id, entity_id)
+            
+            print("\n" + "=" * 50)
+            print("🧪 TEST RESULTS:")
+            print(f"  Schema has CASCADE DELETE: {has_cascade}")
+            print(f"  CASCADE DELETE works: {cascade_works}")
+            
+            if has_cascade and cascade_works:
+                print("✅ PASS: Foreign key constraints are properly configured with CASCADE DELETE")
+            elif not has_cascade and not cascade_works:
+                print("❌ FAIL: Foreign key constraints are missing CASCADE DELETE configuration")
+                print("💡 This confirms issue #254 - migration a1b2c3d4e5f6 is needed")
+            else:
+                print("⚠️  MIXED: Unexpected result combination")
+            
+            return cascade_works
+            
+        except Exception as e:
+            print(f"💥 Test failed with error: {e}")
+            return False
+        finally:
+            await self.cleanup()
+            # Always restore backup to avoid leaving test data
+            await self.restore_backup()
+
+
+async def main():
+    """Main test function."""
+    import argparse
+    
+    parser = argparse.ArgumentParser(description="Test cascade delete on production database")
+    parser.add_argument("--db-path", type=Path, help="Path to database file (default: ~/.basic-memory/memory.db)")
+    parser.add_argument("--no-backup", action="store_true", help="Skip creating backup (dangerous)")
+    
+    args = parser.parse_args()
+    
+    if args.no_backup:
+        print("⚠️  WARNING: Running without backup!")
+        response = input("Are you sure? Type 'yes' to continue: ")
+        if response.lower() != 'yes':
+            print("❌ Aborted")
+            return
+    
+    test = ProductionCascadeTest(args.db_path)
+    success = await test.run_test()
+    
+    sys.exit(0 if success else 1)
+
+
+if __name__ == "__main__":
+    asyncio.run(main())

tests/utils/test_file_utils.py

@@ -3,6 +3,8 @@
 from pathlib import Path
 
 import pytest
+import random
+import string
 
 from basic_memory.file_utils import (
     FileError,
@@ -13,11 +15,24 @@ from basic_memory.file_utils import (
     has_frontmatter,
     parse_frontmatter,
     remove_frontmatter,
+    sanitize_for_filename,
     update_frontmatter,
     write_file_atomic,
 )
 
 
+def get_random_word(length: int = 12, necessary_char: str | None = None) -> str:
+    letters = string.ascii_lowercase
+    word_chars = [random.choice(letters) for i in range(length)]
+
+    if necessary_char and length > 0:
+        # Replace a character at a random position with the necessary character
+        random_pos = random.randint(0, length - 1)
+        word_chars[random_pos] = necessary_char
+
+    return "".join(word_chars)
+
+
 @pytest.mark.asyncio
 async def test_compute_checksum():
     """Test checksum computation."""
@@ -241,3 +256,16 @@ async def test_update_frontmatter_errors(tmp_path: Path):
     nonexistent = tmp_path / "nonexistent" / "test.md"
     with pytest.raises(FileError):
         await update_frontmatter(nonexistent, {"title": "Test"})
+
+
+@pytest.mark.asyncio
+def test_sanitize_for_filename_removes_invalid_characters():
+    # Test all invalid characters listed in the regex
+    invalid_chars = '<>:"|?*'
+
+    # All invalid characters should be replaced
+    for char in invalid_chars:
+        text = get_random_word(length=12, necessary_char=char)
+        sanitized_text = sanitize_for_filename(text)
+
+        assert char not in sanitized_text

tests/utils/test_frontmatter_obsidian_compatible.py

@@ -0,0 +1,183 @@
+"""Tests for Obsidian-compatible YAML frontmatter formatting."""
+
+import frontmatter
+
+from basic_memory.file_utils import dump_frontmatter
+
+
+def test_tags_formatted_as_yaml_list():
+    """Test that tags are formatted as YAML list instead of JSON array."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["type"] = "note"
+    post.metadata["tags"] = ["system", "overview", "reference"]
+    
+    result = dump_frontmatter(post)
+    
+    # Should use YAML list format
+    assert "tags:" in result
+    assert "- system" in result
+    assert "- overview" in result  
+    assert "- reference" in result
+    
+    # Should NOT use JSON array format
+    assert '["system"' not in result
+    assert '"overview"' not in result
+    assert '"reference"]' not in result
+
+
+def test_empty_tags_list():
+    """Test that empty tags list is handled correctly."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["tags"] = []
+    
+    result = dump_frontmatter(post)
+    
+    # Should have empty list representation
+    assert "tags: []" in result
+
+
+def test_single_tag():
+    """Test that single tag is still formatted as list."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["tags"] = ["single-tag"]
+    
+    result = dump_frontmatter(post)
+    
+    assert "tags:" in result
+    assert "- single-tag" in result
+    
+
+def test_no_tags_metadata():
+    """Test that posts without tags work normally."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["type"] = "note"
+    
+    result = dump_frontmatter(post)
+    
+    assert "title: Test Note" in result
+    assert "type: note" in result
+    assert "tags:" not in result
+
+
+def test_no_frontmatter():
+    """Test that posts with no frontmatter just return content."""
+    post = frontmatter.Post("Test content only")
+    
+    result = dump_frontmatter(post)
+    
+    assert result == "Test content only"
+
+
+def test_complex_tags_with_special_characters():
+    """Test tags with hyphens, underscores, and other valid characters."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["tags"] = ["python-test", "api_integration", "v2.0", "nested/tag"]
+    
+    result = dump_frontmatter(post)
+    
+    assert "- python-test" in result
+    assert "- api_integration" in result
+    assert "- v2.0" in result
+    assert "- nested/tag" in result
+
+
+def test_tags_order_preserved():
+    """Test that tag order is preserved in output."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["tags"] = ["zebra", "apple", "banana"]
+    
+    result = dump_frontmatter(post)
+    
+    # Find the positions of each tag in the output
+    zebra_pos = result.find("- zebra")
+    apple_pos = result.find("- apple") 
+    banana_pos = result.find("- banana")
+    
+    # They should appear in the same order as input
+    assert zebra_pos < apple_pos < banana_pos
+
+
+def test_non_tags_lists_also_formatted():
+    """Test that other lists in metadata are also formatted properly."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["authors"] = ["John Doe", "Jane Smith"]
+    post.metadata["keywords"] = ["AI", "machine learning"]
+    
+    result = dump_frontmatter(post)
+    
+    # Authors should be formatted as YAML list
+    assert "authors:" in result
+    assert "- John Doe" in result
+    assert "- Jane Smith" in result
+    
+    # Keywords should be formatted as YAML list
+    assert "keywords:" in result
+    assert "- AI" in result
+    assert "- machine learning" in result
+
+
+def test_mixed_metadata_types():
+    """Test that mixed metadata types are handled correctly."""
+    post = frontmatter.Post("Test content")
+    post.metadata["title"] = "Test Note"
+    post.metadata["tags"] = ["tag1", "tag2"] 
+    post.metadata["created"] = "2024-01-01"
+    post.metadata["priority"] = 5
+    post.metadata["draft"] = True
+    
+    result = dump_frontmatter(post)
+    
+    # Lists should use YAML format
+    assert "tags:" in result
+    assert "- tag1" in result
+    assert "- tag2" in result
+    
+    # Other types should be normal
+    assert "title: Test Note" in result
+    assert "created: '2024-01-01'" in result or "created: 2024-01-01" in result
+    assert "priority: 5" in result
+    assert "draft: true" in result or "draft: True" in result
+
+
+def test_empty_content():
+    """Test posts with empty content but with frontmatter."""
+    post = frontmatter.Post("")
+    post.metadata["title"] = "Empty Note"
+    post.metadata["tags"] = ["empty", "test"]
+    
+    result = dump_frontmatter(post)
+    
+    # Should have frontmatter delimiter
+    assert result.startswith("---")
+    assert result.endswith("---\n")
+    
+    # Should have proper tag formatting
+    assert "- empty" in result
+    assert "- test" in result
+
+
+def test_roundtrip_compatibility():
+    """Test that the formatted output can be parsed back by frontmatter."""
+    original_post = frontmatter.Post("Test content")
+    original_post.metadata["title"] = "Test Note"
+    original_post.metadata["tags"] = ["system", "test", "obsidian"]
+    original_post.metadata["type"] = "note"
+    
+    # Format with our function
+    formatted = dump_frontmatter(original_post)
+    
+    # Parse it back
+    parsed_post = frontmatter.loads(formatted)
+    
+    # Should have same content and metadata
+    assert parsed_post.content == original_post.content
+    assert parsed_post.metadata["title"] == original_post.metadata["title"]
+    assert parsed_post.metadata["tags"] == original_post.metadata["tags"]
+    assert parsed_post.metadata["type"] == original_post.metadata["type"]

tests/utils/test_parse_tags.py

@@ -30,6 +30,11 @@ from basic_memory.utils import parse_tags
         # Mixed whitespace and '#' characters
         ([" #tag1 ", " ##tag2 "], ["tag1", "tag2"]),
         (" #tag1 , ##tag2 ", ["tag1", "tag2"]),
+        # JSON stringified arrays (common AI assistant issue)
+        ('["tag1", "tag2", "tag3"]', ["tag1", "tag2", "tag3"]),
+        ('["system", "overview", "reference"]', ["system", "overview", "reference"]),
+        ('["#tag1", "##tag2"]', ["tag1", "tag2"]),  # JSON array with hash prefixes
+        ('[ "tag1" , "tag2" ]', ["tag1", "tag2"]),  # JSON array with extra spaces
     ],
 )
 def test_parse_tags(input_tags: Union[List[str], str, None], expected: List[str]) -> None:
@@ -48,3 +53,16 @@ def test_parse_tags_special_case() -> None:
 
     result = parse_tags(TagObject())  # pyright: ignore [reportArgumentType]
     assert result == ["tag1", "tag2"]
+
+
+def test_parse_tags_invalid_json() -> None:
+    """Test that invalid JSON strings fall back to comma-separated parsing."""
+    # Invalid JSON should fall back to comma-separated parsing
+    result = parse_tags('[invalid json')
+    assert result == ["[invalid json"]  # Treated as single tag
+    
+    result = parse_tags('[tag1, tag2]')  # Valid bracket format but not JSON
+    assert result == ["[tag1", "tag2]"]  # Split by comma
+    
+    result = parse_tags('["tag1", "tag2"')  # Incomplete JSON
+    assert result == ['["tag1"', '"tag2"']  # Fall back to comma separation

tests/utils/test_permalink_formatting.py

@@ -79,6 +79,9 @@ Testing permalink generation.
         ("archive/François Müller.md", "archive/francois-muller"),
         ("research/Søren Kierkegård.md", "research/soren-kierkegard"),
         ("articles/El Niño.md", "articles/el-nino"),
+        ("ArticlesElNiño.md", "articles-el-nino"),
+        ("articleselniño.md", "articleselnino"),
+        ("articles-El-Niño.md", "articles-el-nino"),
     ],
 )
 def test_latin_accents_transliteration(input_path, expected):