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

.claude/commands/check-health.md

@@ -1,190 +0,0 @@
-# /project:check-health - Project Health Assessment
-
-Comprehensive health check of the Basic Memory project including code quality, test coverage, dependencies, and documentation.
-
-## Usage
-```
-/project:check-health
-```
-
-## Implementation
-
-You are an expert DevOps engineer for the Basic Memory project. When the user runs `/project:check-health`, execute the following comprehensive assessment:
-
-### Step 1: Git Repository Health
-1. **Repository Status**
-   ```bash
-   git status
-   git log --oneline -5
-   git branch -vv
-   ```
-   - Check working directory status
-   - Verify branch alignment with remote
-   - Check recent commit activity
-
-2. **Branch Analysis**
-   - Verify on main branch
-   - Check if ahead/behind remote
-   - Identify any untracked files
-
-### Step 2: Code Quality Assessment
-1. **Linting and Formatting**
-   ```bash
-   uv run ruff check .
-   uv run pyright
-   ```
-   - Count linting issues by severity
-   - Check type annotation coverage
-   - Verify code formatting compliance
-
-2. **Test Suite Health**
-   ```bash
-   uv run pytest --collect-only -q
-   uv run pytest --co -q | wc -l
-   ```
-   - Count total tests
-   - Check for test discovery issues
-   - Verify test structure integrity
-
-### Step 3: Dependency Analysis
-1. **Dependency Health**
-   ```bash
-   uv tree
-   uv lock --dry-run
-   ```
-   - Check for dependency conflicts
-   - Identify outdated dependencies
-   - Verify lock file consistency
-
-2. **Security Scan**
-   ```bash
-   uv run pip-audit --desc
-   ```
-   - Scan for known vulnerabilities
-   - Check dependency licenses
-   - Identify security advisories
-
-### Step 4: Performance Metrics
-1. **Test Performance**
-   ```bash
-   uv run pytest --durations=10
-   ```
-   - Identify slowest tests
-   - Check overall test execution time
-   - Monitor test suite growth
-
-2. **Build Performance**
-   ```bash
-   time uv run python -c "import basic_memory"
-   ```
-   - Check import time
-   - Validate package installation
-   - Monitor startup performance
-
-### Step 5: Documentation Health
-1. **Documentation Coverage**
-   - Check README.md currency
-   - Verify CLI documentation
-   - Validate MCP tool documentation
-   - Check changelog completeness
-
-2. **API Documentation**
-   - Verify docstring coverage
-   - Check type annotation completeness
-   - Validate example code
-
-### Step 6: Project Metrics
-1. **Code Statistics**
-   ```bash
-   find src -name "*.py" | xargs wc -l
-   find tests -name "*.py" | xargs wc -l
-   ```
-   - Lines of code trends
-   - Test-to-code ratio
-   - File organization metrics
-
-## Health Report Format
-
-Generate comprehensive health dashboard:
-
-```
-🏥 Basic Memory Project Health Report
-
-📊 OVERALL HEALTH: 🟢 EXCELLENT (92/100)
-
-🗂️  GIT REPOSITORY
-✅ Clean working directory
-✅ Up to date with origin/main
-✅ Recent commit activity (5 commits this week)
-
-🔍 CODE QUALITY  
-✅ Linting: 0 errors, 2 warnings
-✅ Type checking: 100% coverage
-✅ Formatting: Compliant
-⚠️  Complex functions: 3 need refactoring
-
-🧪 TEST SUITE
-✅ Total tests: 744 
-✅ Test discovery: All tests found
-✅ Coverage: 98.2%
-⚡ Performance: 45.2s (good)
-
-📦 DEPENDENCIES
-✅ Dependencies: Up to date
-✅ Security: No vulnerabilities
-✅ Conflicts: None detected
-⚠️  Outdated: 2 minor updates available
-
-📖 DOCUMENTATION
-✅ README: Current
-✅ API docs: 95% coverage
-⚠️  CLI reference: Needs update
-✅ Changelog: Complete
-
-📈 METRICS
-├── Source code: 15,432 lines
-├── Test code: 8,967 lines  
-├── Test ratio: 58% (excellent)
-└── Complexity: Low (maintainable)
-
-🎯 RECOMMENDATIONS:
-1. Update CLI documentation
-2. Refactor 3 complex functions
-3. Update minor dependencies
-4. Consider splitting large test files
-
-🏆 PROJECT STATUS: Ready for v0.13.0 release!
-```
-
-## Health Scoring
-
-### Excellent (90-100)
-- All quality gates pass
-- High test coverage (>95%)
-- No security issues
-- Documentation current
-
-### Good (75-89)
-- Minor issues present
-- Good test coverage (>90%)
-- No critical security issues
-- Most documentation current
-
-### Needs Attention (60-74)
-- Several quality issues
-- Adequate test coverage (>80%)
-- Minor security concerns
-- Documentation gaps
-
-### Critical (<60)
-- Major quality problems
-- Low test coverage (<80%)
-- Security vulnerabilities
-- Significant documentation issues
-
-## Context
-- Provides comprehensive project overview
-- Identifies potential issues before they become problems
-- Tracks project health trends over time
-- Helps prioritize maintenance tasks
-- Supports release readiness decisions

.claude/commands/commands.md

@@ -1,62 +0,0 @@
-# Basic Memory Custom Commands
-
-This directory contains custom Claude Code slash commands for the Basic Memory project.
-
-## Available Commands
-
-### Release Management (`/project:release:*`)
-- `/project:release:beta` - Create beta releases with automated quality checks
-- `/project:release:release` - Create stable releases with comprehensive validation  
-- `/project:release:release-check` - Pre-flight validation without making changes
-- `/project:release:changelog` - Generate changelog entries from commits
-
-### Development (`/project:*`)
-- `/project:test-coverage` - Run tests with detailed coverage analysis
-- `/project:test-live` - Live testing suite using real Basic Memory installation
-- `/project:lint-fix` - Run comprehensive linting with auto-fix
-- `/project:check-health` - Comprehensive project health assessment
-
-## Command Structure
-
-Commands are organized by functionality:
-```
-.claude/commands/
-├── release/          # Release management commands
-│   ├── beta.md       # /project:release:beta
-│   ├── release.md    # /project:release:release
-│   ├── release-check.md # /project:release:release-check
-│   └── changelog.md  # /project:release:changelog
-├── test-coverage.md  # /project:test-coverage
-├── test-live.md      # /project:test-live
-├── lint-fix.md       # /project:lint-fix
-├── check-health.md   # /project:check-health
-└── commands.md       # This overview file
-```
-
-## Usage
-
-Commands are invoked using the `/project:` prefix:
-- `/project:release:beta v0.13.0b4`
-- `/project:test-coverage mcp`
-- `/project:test-live core`
-- `/project:release:release-check`
-- `/project:check-health`
-
-## Implementation
-
-Each command is implemented as a Markdown file containing structured prompts that:
-1. Validate preconditions
-2. Execute steps in the correct order
-3. Handle errors gracefully  
-4. Provide clear status updates
-5. Return actionable results
-
-## Tooling Integration
-
-Commands leverage existing project tooling:
-- `just check` - Quality checks
-- `just test` - Test suite
-- `just update-deps` - Dependency updates  
-- `uv` - Package management
-- `git` - Version control
-- GitHub Actions - CI/CD pipeline

.claude/commands/lint-fix.md

@@ -1,145 +0,0 @@
-# /project:lint-fix - Comprehensive Code Quality Fix
-
-Run comprehensive linting and auto-fix code quality issues across the codebase.
-
-## Usage
-```
-/project:lint-fix
-```
-
-## Implementation
-
-You are an expert code quality engineer for the Basic Memory project. When the user runs `/project:lint-fix`, execute the following steps:
-
-### Step 1: Pre-flight Check
-1. **Verify Clean Working Directory**
-   ```bash
-   git status --porcelain
-   ```
-   - Check for uncommitted changes
-   - Warn if working directory is not clean
-   - Suggest stashing changes if needed
-
-### Step 2: Import Organization
-1. **Fix Import Order and Cleanup**
-   ```bash
-   uv run ruff check --select I --fix .
-   ```
-   - Sort imports by category (standard, third-party, local)
-   - Remove unused imports
-   - Fix import spacing and organization
-
-### Step 3: Code Formatting
-1. **Apply Consistent Formatting**
-   ```bash
-   uv run ruff format .
-   ```
-   - Format code according to project style
-   - Fix line length issues (100 chars max)
-   - Standardize quotes and spacing
-
-### Step 4: Linting with Auto-fix
-1. **Fix Linting Issues**
-   ```bash
-   uv run ruff check --fix .
-   ```
-   - Auto-fix safe linting issues
-   - Report any remaining manual fixes needed
-   - Focus on code quality and best practices
-
-### Step 5: Type Checking
-1. **Validate Type Annotations**
-   ```bash
-   uv run pyright
-   ```
-   - Check for type errors
-   - Report any missing type annotations
-   - Validate type compatibility
-
-### Step 6: Report Generation
-Generate comprehensive quality report:
-
-```
-🔧 Code Quality Fix Report
-
-✅ FIXES APPLIED:
-├── Import organization: 12 files updated
-├── Code formatting: 8 files reformatted  
-├── Auto-fixable lint issues: 23 issues resolved
-└── Total files processed: 156
-
-⚠️  MANUAL ATTENTION NEEDED:
-├── Type annotations missing in entity_service.py:45
-├── Complex function needs refactoring in sync_service.py:123
-└── Unused variable in test_utils.py:67
-
-🎯 QUALITY SCORE: 96.2% (excellent)
-
-📁 Run `git diff` to review all changes
-```
-
-## Error Handling
-
-### Common Issues
-- **Merge Conflicts**: Provide resolution guidance
-- **Syntax Errors**: Point to specific files and lines
-- **Type Errors**: Suggest specific fixes
-- **Import Errors**: Check for missing dependencies
-
-### Recovery Steps
-- If auto-fixes introduce issues, provide rollback instructions
-- If type checking fails, suggest incremental fixes
-- If tests break, provide debugging guidance
-
-## Quality Gates
-
-### Must Pass
-- [ ] All auto-fixable lint issues resolved
-- [ ] Code formatting consistent
-- [ ] No syntax errors
-- [ ] Import organization clean
-
-### Should Pass (Warnings)
-- [ ] No type checking errors
-- [ ] No complex function warnings
-- [ ] No unused variables/imports
-- [ ] Consistent naming conventions
-
-## Output Examples
-
-### Successful Fix
-```
-🎉 CODE QUALITY IMPROVED!
-
-✅ All auto-fixes applied successfully
-📏 Code formatting: 100% compliant
-🔍 Linting: No issues found
-🏷️  Type checking: All passed
-
-Ready for commit! Use:
-git add -A && git commit -m "style: fix code quality issues"
-```
-
-### Issues Requiring Attention
-```
-⚠️  PARTIAL SUCCESS - MANUAL FIXES NEEDED
-
-✅ Auto-fixes applied: 45 issues
-❌ Manual fixes needed: 3 issues
-
-Priority fixes:
-1. Fix type annotation in services/entity_service.py:142
-2. Simplify complex function in sync/sync_service.py:67
-3. Remove unused import in tests/conftest.py:12
-
-Run these commands:
-# Fix specific file
-uv run pyright src/basic_memory/services/entity_service.py
-```
-
-## Context
-- Uses ruff for fast Python linting and formatting
-- Uses pyright for type checking
-- Follows project code style guidelines (100 char line length)
-- Maintains backward compatibility
-- Integrates with existing pre-commit hooks

.claude/commands/release/changelog.md

@@ -8,7 +8,7 @@ Analyze commits and generate formatted changelog entry for a version.
 ```
 
 **Parameters:**
-- `version` (required): Version like `v0.13.0` or `v0.13.0b4`
+- `version` (required): Version like `v0.14.0` or `v0.14.0b1`
 - `type` (optional): `beta`, `rc`, or `stable` (default: `stable`)
 
 ## Implementation
@@ -59,8 +59,9 @@ You are an expert technical writer for the Basic Memory project. When the user r
 ### Step 3: Generate Changelog Entry
 Create formatted entry following existing CHANGELOG.md style:
 
+Example:
 ```markdown
-## v0.13.0 (2025-06-03)
+## <version> (<date>)
 
 ### Features
 
@@ -128,6 +129,8 @@ Create formatted entry following existing CHANGELOG.md style:
 ## Output Format
 
 ### For Beta Releases
+
+Example: 
 ```markdown
 ## v0.13.0b4 (2025-06-03)
 

.claude/commands/test-coverage.md

@@ -1,131 +0,0 @@
-# /test-coverage - Run Tests with Coverage Analysis
-
-Execute test suite with comprehensive coverage reporting and analysis.
-
-## Usage
-```
-/test-coverage [pattern]
-```
-
-**Parameters:**
-- `pattern` (optional): Test pattern to run specific tests (e.g., `test_mcp`, `*integration*`)
-
-## Implementation
-
-You are an expert QA engineer for the Basic Memory project. When the user runs `/test-coverage`, execute the following steps:
-
-### Step 1: Test Execution
-1. **Run Tests with Coverage**
-   ```bash
-   # Full test suite
-   uv run pytest --cov=basic_memory --cov-report=html --cov-report=term -v
-   
-   # Or with pattern if provided
-   uv run pytest tests/*{pattern}* --cov=basic_memory --cov-report=html --cov-report=term -v
-   ```
-
-2. **Generate Coverage Reports**
-   - Terminal summary with percentages
-   - HTML report for detailed analysis
-   - Identify files below coverage threshold
-
-### Step 2: Coverage Analysis
-1. **Summary Statistics**
-   - Overall coverage percentage
-   - Number of files with 100% coverage
-   - Files below 95% threshold
-   - Total lines covered/missed
-
-2. **Detailed Breakdown**
-   - Coverage by module/package
-   - Identify untested code paths
-   - Find missing edge case tests
-
-### Step 3: Report Generation
-Generate comprehensive coverage report:
-
-```
-🧪 Test Coverage Report
-
-📊 OVERALL COVERAGE: 98.2% (target: 95%+)
-
-✅ EXCELLENT COVERAGE (>95%):
-├── basic_memory/mcp/: 99.1%
-├── basic_memory/services/: 98.8%
-├── basic_memory/repository/: 97.9%
-└── basic_memory/api/: 96.2%
-
-⚠️  NEEDS ATTENTION (<95%):
-├── basic_memory/sync/: 94.1% (missing 12 lines)
-└── basic_memory/importers/: 91.8% (missing 23 lines)
-
-🎯 SPECIFIC GAPS:
-├── sync_service.py:142-145 (error handling)
-├── importer_base.py:67-70 (edge case)
-└── file_utils.py:89 (exception path)
-
-📁 HTML Report: htmlcov/index.html
-🚀 Run `open htmlcov/index.html` to view detailed report
-```
-
-### Step 4: Actionable Recommendations
-1. **Coverage Improvements**
-   - Suggest specific tests to add
-   - Identify edge cases to cover
-   - Recommend integration tests
-
-2. **Quality Insights**
-   - Highlight well-tested modules
-   - Point out testing patterns to follow
-   - Suggest refactoring for testability
-
-## Advanced Analysis
-
-### Performance Metrics
-- Test execution time by module
-- Slowest tests identification
-- Coverage collection overhead
-
-### Integration Coverage
-- MCP tool integration tests
-- API endpoint coverage
-- Database operation coverage
-- File system operation coverage
-
-## Output Examples
-
-### Full Coverage Success
-```
-🎉 EXCELLENT COVERAGE!
-
-📊 Coverage: 98.7% (744 tests passed)
-✅ All modules above 95% threshold
-🏆 23 files with 100% coverage
-⚡ Tests completed in 45.2s
-
-Ready for release! 🚀
-```
-
-### Coverage Issues Found
-```
-⚠️  COVERAGE GAPS DETECTED
-
-📊 Coverage: 92.1% (below 95% target)
-❌ 3 modules need attention
-🔍 43 uncovered lines found
-
-Priority fixes:
-1. Add tests for error handling in sync_service.py
-2. Cover edge cases in importer_base.py
-3. Test exception paths in file_utils.py
-
-Run specific tests:
-uv run pytest tests/sync/ -v
-```
-
-## Context
-- Uses pytest with coverage plugin
-- Generates both terminal and HTML reports
-- Focuses on actionable improvement suggestions
-- Integrates with existing test infrastructure
-- Helps maintain high code quality standards

.claude/commands/test-live.md

@@ -1,6 +1,7 @@
 # /project:test-live - Live Basic Memory Testing Suite
 
-Execute comprehensive real-world testing of Basic Memory using the installed version, following the methodology in TESTING.md. All test results are recorded as notes in a dedicated test project.
+Execute comprehensive real-world testing of Basic Memory using the installed version. 
+All test results are recorded as notes in a dedicated test project.
 
 ## Usage
 ```
@@ -8,12 +9,45 @@ Execute comprehensive real-world testing of Basic Memory using the installed ver
 ```
 
 **Parameters:**
-- `phase` (optional): Specific test phase to run (`core`, `features`, `edge`, `workflows`, `stress`, or `all`)
+- `phase` (optional): Specific test phase to run (`recent`, `core`, `features`, `edge`, `workflows`, `stress`, or `all`)
+- `recent` - Focus on recent changes and new features (recommended for regular testing)
+- `core` - Essential tools only (Tier 1: write_note, read_note, search_notes, edit_note, list_projects, switch_project)
+- `features` - Core + important workflows (Tier 1 + Tier 2)
+- `all` - Comprehensive testing of all tools and scenarios
 
 ## Implementation
 
 You are an expert QA engineer conducting live testing of Basic Memory. 
-When the user runs `/project:test-live`, execute comprehensive testing following the TESTING.md methodology:
+When the user runs `/project:test-live`, execute comprehensive test plan:
+
+## Tool Testing Priority
+
+### **Tier 1: Critical Core (Always Test)**
+1. **write_note** - Foundation of all knowledge creation
+2. **read_note** - Primary knowledge retrieval mechanism  
+3. **search_notes** - Essential for finding information
+4. **edit_note** - Core content modification capability
+5. **list_memory_projects** - Project discovery and status
+6. **switch_project** - Context switching for multi-project workflows
+
+### **Tier 2: Important Workflows (Usually Test)**
+7. **recent_activity** - Understanding what's changed
+8. **build_context** - Conversation continuity via memory:// URLs
+9. **create_memory_project** - Essential for project setup
+10. **move_note** - Knowledge organization
+11. **sync_status** - Understanding system state
+
+### **Tier 3: Enhanced Functionality (Sometimes Test)**
+12. **view_note** - Claude Desktop artifact display
+13. **read_content** - Raw content access
+14. **delete_note** - Content removal
+15. **list_directory** - File system exploration
+16. **set_default_project** - Configuration
+17. **delete_project** - Administrative cleanup
+
+### **Tier 4: Specialized (Rarely Test)**
+18. **canvas** - Obsidian visualization (specialized use case)
+19. **MCP Prompts** - Enhanced UX tools (ai_assistant_guide, continue_conversation)
 
 ### Pre-Test Setup
 
@@ -22,7 +56,13 @@ When the user runs `/project:test-live`, execute comprehensive testing following
    - Check version and confirm it's the expected release
    - Test MCP connection and tool availability
 
-2. **Test Project Creation**
+2. **Recent Changes Analysis** (if phase includes 'recent' or 'all')
+   - Run `git log --oneline -20` to examine recent commits
+   - Identify new features, bug fixes, and enhancements
+   - Generate targeted test scenarios for recent changes
+   - Prioritize regression testing for recently fixed issues
+
+3. **Test Project Creation**
 
 Run the bash `date` command to get the current date/time. 
 
@@ -34,83 +74,158 @@ Run the bash `date` command to get the current date/time.
 
 Make sure to switch to the newly created project with the `switch_project()` tool.
 
-3. **Baseline Documentation**
+4. **Baseline Documentation**
    Create initial test session note with:
    - Test environment details
    - Version being tested
+   - Recent changes identified (if applicable)
    - Test objectives and scope
    - Start timestamp
 
-### Phase 1: Core Functionality Validation
+### Phase 0: Recent Changes Validation (if 'recent' or 'all' phase)
 
-Test all fundamental MCP tools systematically:
+Based on recent commit analysis, create targeted test scenarios:
 
-**write_note Tests:**
-- Basic note creation with various content types
-- Frontmatter handling (tags, custom fields)
-- Special characters in titles and content
-- Unicode and emoji support
-- Empty notes and minimal content
+**Recent Changes Test Protocol:**
+1. **Feature Addition Tests** - For each new feature identified:
+   - Test basic functionality
+   - Test integration with existing tools
+   - Verify documentation accuracy
+   - Test edge cases and error handling
 
-**read_note Tests:**
-- Read by title, permalink, memory:// URLs
-- Non-existent notes (error handling)
-- Notes with complex formatting
-- Performance with large notes
+2. **Bug Fix Regression Tests** - For each recent fix:
+   - Recreate the original problem scenario
+   - Verify the fix works as expected
+   - Test related functionality isn't broken
+   - Document the verification in test notes
 
-**view_note Tests:**
-- View notes as formatted artifacts (Claude Desktop)
-- Title extraction from frontmatter and headings
-- Unicode and emoji content in artifacts
-- Error handling for non-existent notes
-- Artifact display quality and readability
+3. **Performance/Enhancement Validation** - For optimizations:
+   - Establish baseline timing
+   - Compare with expected improvements
+   - Test under various load conditions
+   - Document performance observations
 
-**search_notes Tests:**
-- Simple text queries
-- Tag-based searches 
-- Boolean operators and complex queries
-- Empty/no results scenarios
-- Performance with growing knowledge base
+**Example Recent Changes (Update based on actual git log):**
+- Watch Service Restart (#156): Test project creation → file modification → automatic restart
+- Cross-Project Moves (#161): Test move_note with cross-project detection
+- Docker Environment Support (#174): Test BASIC_MEMORY_HOME behavior
+- MCP Server Logging (#164): Verify log level configurations
 
-**Recent Activity Tests:**
-- Various timeframes ("today", "1 week", "1d")
-- Type filtering (if available)
-- Empty project scenarios
-- Performance with many recent changes
+### Phase 1: Core Functionality Validation (Tier 1 Tools)
 
-**Context Building Tests:**
-- Different depth levels (1, 2, 3+)
-- Various timeframes
-- Relation traversal accuracy
-- Performance with complex graphs
+Test essential MCP tools that form the foundation of Basic Memory:
 
-### Phase 2: v0.13.0 Feature Deep Dive
+**1. write_note Tests (Critical):**
+- ✅ Basic note creation with frontmatter
+- ✅ Special characters and Unicode in titles
+- ✅ Various content types (lists, headings, code blocks)
+- ✅ Empty notes and minimal content edge cases
+- ⚠️ Error handling for invalid parameters
 
-**Project Management:**
-- Create multiple projects dynamically
-- Switch between projects mid-conversation  
-- Cross-project operations
-- Project discovery and status
-- Default project behavior
-- Invalid project handling
+**2. read_note Tests (Critical):**
+- ✅ Read by title, permalink, memory:// URLs
+- ✅ Non-existent notes (error handling)
+- ✅ Notes with complex markdown formatting
+- ⚠️ Performance with large notes (>10MB)
 
-**Advanced Note Editing:**
-- `edit_note` with append operations
-- Prepend operations
-- Find/replace with validation
-- Section replacement under headers
-- Error scenarios (invalid operations)
-- Frontmatter preservation
+**3. search_notes Tests (Critical):**
+- ✅ Simple text queries across content
+- ✅ Tag-based searches with multiple tags
+- ✅ Boolean operators (AND, OR, NOT)
+- ✅ Empty/no results scenarios
+- ⚠️ Performance with 100+ notes
 
-**File Management:**
-- `move_note` within same project
-- Move between projects
-- Automatic folder creation
-- Special characters in paths
-- Database consistency validation
-- Search index updates after moves
+**4. edit_note Tests (Critical):**
+- ✅ Append operations preserving frontmatter
+- ✅ Prepend operations
+- ✅ Find/replace with validation
+- ✅ Section replacement under headers
+- ⚠️ Error scenarios (invalid operations)
 
-### Phase 3: Edge Case Exploration
+**5. list_memory_projects Tests (Critical):**
+- ✅ Display all projects with status indicators
+- ✅ Current and default project identification
+- ✅ Empty project list handling
+- ✅ Project metadata accuracy
+
+**6. switch_project Tests (Critical):**
+- ✅ Switch between existing projects
+- ✅ Context preservation during switch
+- ⚠️ Invalid project name handling
+- ✅ Confirmation of successful switch
+
+### Phase 2: Important Workflows (Tier 2 Tools)
+
+**7. recent_activity Tests (Important):**
+- ✅ Various timeframes ("today", "1 week", "1d")
+- ✅ Type filtering capabilities
+- ✅ Empty project scenarios
+- ⚠️ Performance with many recent changes
+
+**8. build_context Tests (Important):**
+- ✅ Different depth levels (1, 2, 3+)
+- ✅ Various timeframes for context
+- ✅ memory:// URL navigation
+- ⚠️ Performance with complex relation graphs
+
+**9. create_memory_project Tests (Important):**
+- ✅ Create projects dynamically
+- ✅ Set default during creation
+- ✅ Path validation and creation
+- ⚠️ Invalid paths and names
+- ✅ Integration with existing projects
+
+**10. move_note Tests (Important):**
+- ✅ Move within same project
+- ✅ Cross-project moves with detection (#161)
+- ✅ Automatic folder creation
+- ✅ Database consistency validation
+- ⚠️ Special characters in paths
+
+**11. sync_status Tests (Important):**
+- ✅ Background operation monitoring
+- ✅ File synchronization status
+- ✅ Project sync state reporting
+- ⚠️ Error state handling
+
+### Phase 3: Enhanced Functionality (Tier 3 Tools)
+
+**12. view_note Tests (Enhanced):**
+- ✅ Claude Desktop artifact display
+- ✅ Title extraction from frontmatter
+- ✅ Unicode and emoji content rendering
+- ⚠️ Error handling for non-existent notes
+
+**13. read_content Tests (Enhanced):**
+- ✅ Raw file content access
+- ✅ Binary file handling
+- ✅ Image file reading
+- ⚠️ Large file performance
+
+**14. delete_note Tests (Enhanced):**
+- ✅ Single note deletion
+- ✅ Database consistency after deletion
+- ⚠️ Non-existent note handling
+- ✅ Confirmation of successful deletion
+
+**15. list_directory Tests (Enhanced):**
+- ✅ Directory content listing
+- ✅ Depth control and filtering
+- ✅ File name globbing
+- ⚠️ Empty directory handling
+
+**16. set_default_project Tests (Enhanced):**
+- ✅ Change default project
+- ✅ Configuration persistence
+- ⚠️ Invalid project handling
+
+**17. delete_project Tests (Enhanced):**
+- ✅ Project removal from config
+- ✅ Database cleanup
+- ⚠️ Default project protection
+- ⚠️ Non-existent project handling
+
+### Phase 4: Edge Case Exploration
 
 **Boundary Testing:**
 - Very long titles and content (stress limits)
@@ -134,7 +249,7 @@ Test all fundamental MCP tools systematically:
 - Rapid successive operations
 - Memory usage monitoring
 
-### Phase 4: Real-World Workflow Scenarios
+### Phase 5: Real-World Workflow Scenarios
 
 **Meeting Notes Pipeline:**
 1. Create meeting notes with action items
@@ -164,7 +279,35 @@ Test all fundamental MCP tools systematically:
 4. Update content with edit operations
 5. Validate knowledge graph integrity
 
-### Phase 5: Creative Stress Testing
+### Phase 6: Specialized Tools Testing (Tier 4)
+
+**18. canvas Tests (Specialized):**
+- ✅ JSON Canvas generation
+- ✅ Node and edge creation
+- ✅ Obsidian compatibility
+- ⚠️ Complex graph handling
+
+**19. MCP Prompts Tests (Specialized):**
+- ✅ ai_assistant_guide output
+- ✅ continue_conversation functionality
+- ✅ Formatted search results
+- ✅ Enhanced activity reports
+
+### Phase 7: Integration & File Watching Tests
+
+**File System Integration:**
+- ✅ Watch service behavior with file changes
+- ✅ Project creation → watch restart (#156)
+- ✅ Multi-project synchronization
+- ⚠️ MCP→API→DB→File stack validation
+
+**Real Integration Testing:**
+- ✅ End-to-end file watching vs manual operations
+- ✅ Cross-session persistence
+- ✅ Database consistency across operations
+- ⚠️ Performance under real file system changes
+
+### Phase 8: Creative Stress Testing
 
 **Creative Exploration:**
 - Rapid project creation/switching patterns
@@ -180,6 +323,26 @@ Test all fundamental MCP tools systematically:
 - Complex boolean search expressions
 - Resource constraint testing
 
+## Test Execution Guidelines
+
+### Quick Testing (core/features phases)
+- Focus on Tier 1 tools (core) or Tier 1+2 (features)
+- Test essential functionality and common edge cases
+- Record critical issues immediately
+- Complete in 15-20 minutes
+
+### Comprehensive Testing (all phase)
+- Cover all tiers systematically
+- Include specialized tools and stress testing
+- Document performance baselines
+- Complete in 45-60 minutes
+
+### Recent Changes Focus (recent phase)
+- Analyze git log for recent commits
+- Generate targeted test scenarios
+- Focus on regression testing for fixes
+- Validate new features thoroughly
+
 ## Test Observation Format
 
 Record ALL observations immediately as Basic Memory notes:
@@ -202,14 +365,14 @@ permalink: test-session-[phase]-[timestamp]
 ## Test Results
 
 ### ✅ Successful Operations
-- [timestamp] write_note: Created note with emoji title 📝 #functionality
-- [timestamp] search_notes: Boolean query returned 23 results in 0.4s #performance  
-- [timestamp] edit_note: Append operation preserved frontmatter #reliability
+- [timestamp] ✅ write_note: Created note with emoji title 📝 #tier1 #functionality
+- [timestamp] ✅ search_notes: Boolean query returned 23 results in 0.4s #tier1 #performance  
+- [timestamp] ✅ edit_note: Append operation preserved frontmatter #tier1 #reliability
 
 ### ⚠️ Issues Discovered
-- [timestamp] move_note: Slow with deep folder paths (2.1s) #performance
-- [timestamp] search_notes: Unicode query returned unexpected results #bug
-- [timestamp] project switch: Context lost for memory:// URLs #issue
+- [timestamp] ⚠️ move_note: Slow with deep folder paths (2.1s) #tier2 #performance
+- [timestamp] 🚨 search_notes: Unicode query returned unexpected results #tier1 #bug #critical
+- [timestamp] ⚠️ build_context: Context lost for memory:// URLs #tier2 #issue
 
 ### 🚀 Enhancements Identified
 - edit_note could benefit from preview mode #ux-improvement
@@ -353,24 +516,44 @@ For each error discovered:
    - Create comprehensive summary report
    - Generate development recommendations
 
+## Testing Success Criteria
+
+### Core Testing (Tier 1) - Must Pass
+- All 6 critical tools function correctly
+- No critical bugs in essential workflows
+- Acceptable performance for basic operations
+- Error handling works as expected
+
+### Feature Testing (Tier 1+2) - Should Pass
+- All 11 core + important tools function
+- Workflow scenarios complete successfully
+- Performance meets baseline expectations
+- Integration points work correctly
+
+### Comprehensive Testing (All Tiers) - Complete Coverage
+- All tools tested across all scenarios
+- Edge cases and stress testing completed
+- Performance baselines established
+- Full documentation of issues and enhancements
+
 ## Expected Outcomes
 
 **System Validation:**
-- v0.13.0 feature verification in real usage
-- Edge case discovery beyond unit tests
+- Feature verification prioritized by tier importance
+- Recent changes validated for regression
 - Performance baseline establishment
-- Bug identification with reproduction cases
+- Bug identification with severity assessment
 
 **Knowledge Base Creation:**
-- Comprehensive testing documentation
+- Prioritized testing documentation
 - Real usage examples for user guides
-- Edge case scenarios for future testing
+- Recent changes validation records
 - Performance insights for optimization
 
 **Development Insights:**
-- Prioritized bug fix list
+- Tier-based bug priority list
+- Recent changes impact assessment
 - Enhancement ideas from real usage
-- Architecture validation results
 - User experience improvement areas
 
 ## Post-Test Deliverables
@@ -402,9 +585,11 @@ For each error discovered:
    - Add performance benchmarks and targets
 
 ## Context
-- Uses installed basic-memory version (not development)
+- Uses real installed basic-memory version 
 - Tests complete MCP→API→DB→File stack
 - Creates living documentation in Basic Memory itself
 - Follows integration over isolation philosophy
+- Prioritizes testing by tool importance and usage frequency
+- Adapts to recent development changes dynamically
 - Focuses on real usage patterns over checklist validation
-- Generates actionable insights for development team
+- Generates actionable insights prioritized by impact

.github/workflows/claude.yml

@@ -111,4 +111,4 @@ jobs:
         uses: anthropics/claude-code-action@beta
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
-          allowed_tools: Bash(uv run pytest),Bash(uv run ruff check . --fix),Bash(uv run ruff format .),Bash(uv run pyright),Bash(just test),Bash(just lint),Bash(just format),Bash(just type-check),Bash(just check),Read,Write,Edit,MultiEdit,Glob,Grep,LS
+          allowed_tools: Bash(uv run pytest),Bash(uv run ruff check . --fix),Bash(uv run ruff format .),Bash(uv run pyright),Bash(just test),Bash(just lint),Bash(just format),Bash(just type-check),Bash(just check),Read,Write,Edit,MultiEdit,Glob,Grep,LS, mcp__web_search

.github/workflows/release.yml

@@ -57,6 +57,8 @@ jobs:
     name: Update Homebrew Formula
     needs: release
     runs-on: ubuntu-latest
+    # Only run for stable releases (not dev, beta, or rc versions)
+    if: ${{ !contains(github.ref_name, 'dev') && !contains(github.ref_name, 'b') && !contains(github.ref_name, 'rc') }}
     permissions:
       contents: write
       actions: read
@@ -80,3 +82,4 @@ jobs:
         env:
           # Personal Access Token with repo scope for homebrew-basic-memory repo
           COMMITTER_TOKEN: ${{ secrets.HOMEBREW_TOKEN }}
+

.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

.mcp.json

@@ -1,14 +0,0 @@
-{
-  "mcpServers": {
-    "basic-memory": {
-      "command": "uv",
-      "args": [
-        "--directory",
-        "/Users/phernandez/dev/basicmachines/basic-memory",
-        "run",
-        "src/basic_memory/cli/main.py",
-        "mcp"
-      ]
-    }
-  }
-}

CHANGELOG.md

@@ -1,56 +1,184 @@
 # CHANGELOG
 
-## v0.13.8 (2025-06-20)
-
-### Features
-
-- **Docker Container Support** - Complete Docker integration with volume mounting for Obsidian directories
-  ([`3269a2f`](https://github.com/basicmachines-co/basic-memory/commit/3269a2f33a7595f6d9e5207924062e2542f46759))
-  - Docker Compose configuration for easy deployment
-  - Volume mounting for persistent data and Obsidian integration
-  - Comprehensive Docker documentation and setup guides
-  - Streamlined container-based workflow
+## v0.14.2 (2025-07-03)
 
 ### Bug Fixes
 
-- **#151**: Fix reset command project configuration persistence issue
-  ([`af44941`](https://github.com/basicmachines-co/basic-memory/commit/af44941d5aa57b5ad7fcc6af4ed700f49bdb6d4d))
-  - Reset command now properly clears project configuration from `~/.basic-memory/config.json`
-  - Eliminates issue where projects would be recreated after database reset
-  - Ensures clean slate when resetting Basic Memory installation
+- **#204**: Fix MCP Error with MCP-Hub integration
+  ([`3621bb7`](https://github.com/basicmachines-co/basic-memory/commit/3621bb7b4d6ac12d892b18e36bb8f7c9101c7b10))
+  - Resolve compatibility issues with MCP-Hub
+  - Improve error handling in project management tools
+  - Ensure stable MCP tool integration across different environments
 
-- **#148**: Resolve project state inconsistency between MCP and CLI
-  ([`35e4f73`](https://github.com/basicmachines-co/basic-memory/commit/35e4f73ae8a65501da4d48258ed702f957184c92))
-  - Fix "Project not found" errors when switching default projects
-  - MCP session now automatically refreshes when project configuration changes
-  - Eliminates need to restart MCP server after project operations
-  - Ensures consistent project state across CLI and MCP interfaces
+- **Modernize datetime handling and suppress SQLAlchemy warnings**
+  ([`f80ac0e`](https://github.com/basicmachines-co/basic-memory/commit/f80ac0e3e74b7a737a7fc7b956b5c1d61b0c67b8))
+  - Replace deprecated `datetime.utcnow()` with timezone-aware alternatives
+  - Suppress SQLAlchemy deprecation warnings for cleaner output
+  - Improve future compatibility with Python datetime best practices
 
-- **FastMCP Compatibility** - Resolve deprecation warnings for FastMCP integration
-  ([`7be001c`](https://github.com/basicmachines-co/basic-memory/commit/7be001ca6834b3344bb6160cbe537b36bcbaa579))
-  - Update FastMCP usage patterns to eliminate deprecation warnings
-  - Improve future compatibility with FastMCP library updates
-  - Clean up entity repository and service layer code
+## v0.14.1 (2025-07-03)
+
+### Bug Fixes
+
+- **#203**: Constrain fastmcp version to prevent breaking changes
+  ([`827f7cf`](https://github.com/basicmachines-co/basic-memory/commit/827f7cf86e7b84c56e7a43bb83f2e5d84a1ad8b8))
+  - Pin fastmcp to compatible version range to avoid API breaking changes
+  - Ensure stable MCP server functionality across updates
+  - Improve dependency management for production deployments
+
+- **#190**: Fix Problems with MCP integration  
+  ([`bd4f551`](https://github.com/basicmachines-co/basic-memory/commit/bd4f551a5bb0b7b4d3a5b04de70e08987c6ab2f9))
+  - Resolve MCP server initialization and communication issues
+  - Improve error handling and recovery in MCP operations
+  - Enhance stability for AI assistant integrations
+
+### Features
+
+- **Add Cursor IDE integration button** - One-click setup for Cursor IDE users
+  ([`5360005`](https://github.com/basicmachines-co/basic-memory/commit/536000512294d66090bf87abc8014f4dfc284310))
+  - Direct installation button for Cursor IDE in README
+  - Streamlined setup process for Cursor users
+  - Enhanced developer experience for AI-powered coding
+
+- **Add Homebrew installation instructions** - Official Homebrew tap support
+  ([`39f811f`](https://github.com/basicmachines-co/basic-memory/commit/39f811f8b57dd998445ae43537cd492c680b2e11))
+  - Official Homebrew formula in basicmachines-co/basic-memory tap
+  - Simplified installation process for macOS users
+  - Package manager integration for easier dependency management
+
+## v0.14.0 (2025-06-26)
+
+### Features
+
+- **Docker Container Registry Migration** - Switch from Docker Hub to GitHub Container Registry for better security and integration  
+  ([`616c1f0`](https://github.com/basicmachines-co/basic-memory/commit/616c1f0710da59c7098a5f4843d4f017877ff7b2))
+  - Automated Docker image publishing via GitHub Actions CI/CD pipeline
+  - Enhanced container security with GitHub's integrated vulnerability scanning
+  - Streamlined container deployment workflow for production environments
+
+- **Enhanced Search Documentation** - Comprehensive search syntax examples for improved user experience
+  ([`a589f8b`](https://github.com/basicmachines-co/basic-memory/commit/a589f8b894e78cce01eb25656856cfea8785fbbf))
+  - Detailed examples for Boolean search operators (AND, OR, NOT)
+  - Advanced search patterns including phrase matching and field-specific queries
+  - User-friendly documentation for complex search scenarios
+
+- **Cross-Project File Management** - Intelligent move operations with project boundary detection
+  ([`db5ef7d`](https://github.com/basicmachines-co/basic-memory/commit/db5ef7d35cc0894309c7a57b5741c9dd978526d4))
+  - Automatic detection of cross-project move attempts with helpful guidance
+  - Clear error messages when attempting unsupported cross-project operations
+
+### Bug Fixes
+
+- **#184**: Preserve permalinks when editing notes without frontmatter permalinks
+  ([`c2f4b63`](https://github.com/basicmachines-co/basic-memory/commit/c2f4b632cf04921b1a3c2f0d43831b80c519cb31))
+  - Fix permalink preservation during note editing operations
+  - Ensure consistent permalink handling across different note formats
+  - Maintain note identity and searchability during incremental edits
+
+- **#183**: Implement project-specific sync status checks for MCP tools
+  ([`12b5152`](https://github.com/basicmachines-co/basic-memory/commit/12b51522bc953fca117fc5bc01fcb29c6ca7e13c))
+  - Fix sync status reporting to correctly reflect current project state
+  - Resolve inconsistencies where sync status showed global instead of project-specific information
+  - Improve project isolation for sync operations and status reporting
+
+- **#180**: Handle Boolean search syntax with hyphenated terms
+  ([`546e3cd`](https://github.com/basicmachines-co/basic-memory/commit/546e3cd8db98b74f746749d41887f8a213cd0b11))
+  - Fix search parsing issues with hyphenated terms in Boolean queries
+  - Improve search query tokenization for complex term structures
+  - Enhanced search reliability for technical documentation and multi-word concepts
+
+- **#174**: Respect BASIC_MEMORY_HOME environment variable in Docker containers
+  ([`9f1db23`](https://github.com/basicmachines-co/basic-memory/commit/9f1db23c78d4648e2c242ad1ee27eed85e3f3b5d))
+  - Fix Docker container configuration to properly honor custom home directory settings
+  - Improve containerized deployment flexibility with environment variable support
+  - Ensure consistent behavior between local and containerized installations
+
+- **#168**: Scope entity queries by project_id in upsert_entity method
+  ([`2a3adc1`](https://github.com/basicmachines-co/basic-memory/commit/2a3adc109a3e4d7ccd65cae4abf63d9bb2338326))
+  - Fix entity isolation issues in multi-project setups
+  - Prevent cross-project entity conflicts during database operations
+  - Strengthen project boundary enforcement at the database level
+
+- **#166**: Handle None from_entity in Context API RelationSummary
+  ([`8a065c3`](https://github.com/basicmachines-co/basic-memory/commit/8a065c32f4e41613207d29aafc952a56e3a52241))
+  - Fix null pointer exceptions in relation processing
+  - Improve error handling for incomplete relation data
+  - Enhanced stability for knowledge graph traversal operations
+
+- **#164**: Remove log level configuration from mcp_server.run()
+  ([`224e4bf`](https://github.com/basicmachines-co/basic-memory/commit/224e4bf9e4438c44a82ffc21bd1a282fe9087690))
+  - Simplify MCP server startup by removing redundant log level settings
+  - Fix potential logging configuration conflicts
+  - Streamline server initialization process
+
+- **#162**: Ensure permalinks are generated for entities with null permalinks during move operations
+  ([`f506507`](https://github.com/basicmachines-co/basic-memory/commit/f50650763dbd4322c132e4bdc959ce4bf074374b))
+  - Fix move operations for entities without existing permalinks
+  - Automatic permalink generation during file move operations
+  - Maintain database consistency during file reorganization
 
 ### Technical Improvements
 
-- **Comprehensive Integration Testing** - New test suites for critical user workflows
-  - Full integration tests for database reset functionality
-  - End-to-end project state synchronization testing
-  - Real MCP client-server communication validation
-  - Direct config file validation without complex mocking
+- **Comprehensive Test Coverage** - Extensive test suites for new features and edge cases
+  - Enhanced test coverage for project-specific sync status functionality
+  - Additional test scenarios for search syntax validation and edge cases
+  - Integration tests for Docker CI workflow and container publishing
+  - Comprehensive move operations testing with project boundary validation
 
-- **Code Quality** - Enhanced error handling and validation
-  - Improved project state management across system components
-  - Better session refresh patterns for configuration changes
-  - Streamlined Docker setup with reduced image size
+- **Docker CI/CD Pipeline** - Production-ready automated container publishing
+  ([`74847cc`](https://github.com/basicmachines-co/basic-memory/commit/74847cc3807b0c6ed511e0d83e0d560e9f07ec44))
+  - Automated Docker image building and publishing on release
+  - Multi-architecture container support for AMD64 and ARM64 platforms
+  - Integrated security scanning and vulnerability assessments
+  - Streamlined deployment pipeline for production environments
 
-### Documentation
+- **Release Process Improvements** - Enhanced automation and quality gates
+  ([`a52ce1c`](https://github.com/basicmachines-co/basic-memory/commit/a52ce1c8605ec2cd450d1f909154172cbc30faa2))
+  - Homebrew formula updates limited to stable releases only
+  - Improved release automation with better quality control
+  - Enhanced CI/CD pipeline reliability and error handling
 
-- **Docker Integration Guide** - Complete documentation for container deployment
-  - Step-by-step Docker Compose setup instructions
-  - Volume mounting configuration for Obsidian workflows
-  - Container-based development environment setup
+- **Code Quality Enhancements** - Improved error handling and validation
+  - Better null safety in entity and relation processing
+  - Enhanced project isolation validation throughout the codebase
+  - Improved error messages and user guidance for edge cases
+  - Strengthened database consistency guarantees across operations
+
+### Infrastructure
+
+- **GitHub Container Registry Integration** - Modern container infrastructure
+  - Migration from Docker Hub to GitHub Container Registry (ghcr.io)
+  - Improved security with integrated vulnerability scanning
+  - Better integration with GitHub-based development workflow
+  - Enhanced container versioning and artifact management
+
+- **Enhanced CI/CD Workflows** - Robust automated testing and deployment
+  - Automated Docker image publishing on releases
+  - Comprehensive test coverage validation before deployment
+  - Multi-platform container building and publishing
+  - Integration with GitHub's security and monitoring tools
+
+### Migration Guide
+
+This release includes several behind-the-scenes improvements and fixes. All changes are backward compatible:
+
+- **Docker Users**: Container images now served from `ghcr.io/basicmachines-co/basic-memory` instead of Docker Hub
+- **Search Users**: Enhanced search syntax handling - existing queries continue to work unchanged
+- **Multi-Project Users**: Improved project isolation - all existing projects remain fully functional
+- **All Users**: Enhanced stability and error handling - no breaking changes to existing workflows
+
+### Installation
+
+```bash
+# Latest stable release
+uv tool install basic-memory
+
+# Update existing installation  
+uv tool upgrade basic-memory
+
+# Docker (new registry)
+docker pull ghcr.io/basicmachines-co/basic-memory:latest
+```
 
 ## v0.13.7 (2025-06-19)
 

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
 
@@ -183,73 +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
-- 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.

CONTRIBUTING.md

@@ -27,7 +27,12 @@ project and how to get started as a developer.
 
    > **Note**: Basic Memory uses [just](https://just.systems) as a modern command runner. Install with `brew install just` or `cargo install just`.
 
-3. **Run the Tests**:
+3. **Activate the Virtual Environment**
+   ```bash
+   source .venv/bin/activate
+   ```
+
+4. **Run the Tests**:
    ```bash
    # Run all tests
    just test

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
 
@@ -64,7 +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.
+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
 
@@ -155,8 +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:
 
@@ -266,13 +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)`.
 
@@ -302,6 +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/):
@@ -325,8 +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
@@ -336,9 +327,9 @@ config:
       "command": "uvx",
       "args": [
         "basic-memory",
+        "mcp",
         "--project",
-        "your-project-name",
-        "mcp"
+        "your-project-name"
       ]
     }
   }
@@ -347,27 +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:
@@ -378,10 +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
@@ -393,49 +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
@@ -453,4 +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/).

docs/character-handling.md

@@ -0,0 +1,241 @@
+# Character Handling and Conflict Resolution
+
+Basic Memory handles various character encoding scenarios and file naming conventions to provide consistent permalink generation and conflict resolution. This document explains how the system works and how to resolve common character-related issues.
+
+## Overview
+
+Basic Memory uses a sophisticated system to generate permalinks from file paths while maintaining consistency across different operating systems and character encodings. The system normalizes file paths and generates unique permalinks to prevent conflicts.
+
+## Character Normalization Rules
+
+### 1. Permalink Generation
+
+When Basic Memory processes a file path, it applies these normalization rules:
+
+```
+Original: "Finance/My Investment Strategy.md"
+Permalink: "finance/my-investment-strategy"
+```
+
+**Transformation process:**
+1. Remove file extension (`.md`)
+2. Convert to lowercase (case-insensitive)
+3. Replace spaces with hyphens
+4. Replace underscores with hyphens
+5. Handle international characters (transliteration for Latin, preservation for non-Latin)
+6. Convert camelCase to kebab-case
+
+### 2. International Character Support
+
+**Latin characters with diacritics** are transliterated:
+- `ø` → `o` (Søren → soren)
+- `ü` → `u` (Müller → muller)
+- `é` → `e` (Café → cafe)
+- `ñ` → `n` (Niño → nino)
+
+**Non-Latin characters** are preserved:
+- Chinese: `中文/测试文档.md` → `中文/测试文档`
+- Japanese: `日本語/文書.md` → `日本語/文書`
+
+## Common Conflict Scenarios
+
+### 1. Hyphen vs Space Conflicts
+
+**Problem:** Files with existing hyphens conflict with generated permalinks from spaces.
+
+**Example:**
+```
+File 1: "basic memory bug.md"     → permalink: "basic-memory-bug"
+File 2: "basic-memory-bug.md"    → permalink: "basic-memory-bug" (CONFLICT!)
+```
+
+**Resolution:** The system automatically resolves this by adding suffixes:
+```
+File 1: "basic memory bug.md"     → permalink: "basic-memory-bug"
+File 2: "basic-memory-bug.md"    → permalink: "basic-memory-bug-1"
+```
+
+**Best Practice:** Choose consistent naming conventions within your project.
+
+### 2. Case Sensitivity Conflicts
+
+**Problem:** Different case variations that normalize to the same permalink.
+
+**Example on macOS:**
+```
+Directory: Finance/investment.md
+Directory: finance/investment.md  (different on filesystem, same permalink)
+```
+
+**Resolution:** Basic Memory detects case conflicts and prevents them during sync operations with helpful error messages.
+
+**Best Practice:** Use consistent casing for directory and file names.
+
+### 3. Character Encoding Conflicts
+
+**Problem:** Different Unicode normalizations of the same logical character.
+
+**Example:**
+```
+File 1: "café.md" (é as single character)
+File 2: "café.md" (e + combining accent)
+```
+
+**Resolution:** Basic Memory normalizes Unicode characters using NFD normalization to detect these conflicts.
+
+### 4. Forward Slash Conflicts
+
+**Problem:** Forward slashes in frontmatter or file names interpreted as path separators.
+
+**Example:**
+```yaml
+---
+permalink: finance/investment/strategy
+---
+```
+
+**Resolution:** Basic Memory validates frontmatter permalinks and warns about path separator conflicts.
+
+## Error Messages and Troubleshooting
+
+### "UNIQUE constraint failed: entity.file_path, entity.project_id"
+
+**Cause:** Two entities trying to use the same file path within a project.
+
+**Common scenarios:**
+1. File move operation where destination is already occupied
+2. Case sensitivity differences on macOS
+3. Character encoding conflicts
+4. Concurrent file operations
+
+**Resolution steps:**
+1. Check for duplicate file names with different cases
+2. Look for files with similar names but different character encodings
+3. Rename conflicting files to have unique names
+4. Run sync again after resolving conflicts
+
+### "File path conflict detected during move"
+
+**Cause:** Enhanced conflict detection preventing potential database integrity violations.
+
+**What this means:** The system detected that moving a file would create a conflict before attempting the database operation.
+
+**Resolution:** Follow the specific guidance in the error message, which will indicate the type of conflict detected.
+
+## Best Practices
+
+### 1. File Naming Conventions
+
+**Recommended patterns:**
+- Use consistent casing (prefer lowercase)
+- Use hyphens instead of spaces for multi-word files
+- Avoid special characters that could conflict with path separators
+- Be consistent with directory structure casing
+
+**Examples:**
+```
+✅ Good:
+- finance/investment-strategy.md
+- projects/basic-memory-features.md
+- docs/api-reference.md
+
+❌ Problematic:
+- Finance/Investment Strategy.md  (mixed case, spaces)
+- finance/Investment Strategy.md  (inconsistent case)
+- docs/API/Reference.md          (mixed case directories)
+```
+
+### 2. Permalink Management
+
+**Custom permalinks in frontmatter:**
+```yaml
+---
+type: knowledge
+permalink: custom-permalink-name
+---
+```
+
+**Guidelines:**
+- Use lowercase permalinks
+- Use hyphens for word separation
+- Avoid path separators unless creating sub-paths
+- Ensure uniqueness within your project
+
+### 3. Directory Structure
+
+**Consistent casing:**
+```
+✅ Good:
+finance/
+  investment-strategies.md
+  portfolio-management.md
+
+❌ Problematic:  
+Finance/           (capital F)
+  investment-strategies.md
+finance/           (lowercase f) 
+  portfolio-management.md
+```
+
+## Migration and Cleanup
+
+### Identifying Conflicts
+
+Use Basic Memory's built-in conflict detection:
+
+```bash
+# Sync will report conflicts
+basic-memory sync
+
+# Check sync status for warnings
+basic-memory status
+```
+
+### Resolving Existing Conflicts
+
+1. **Identify conflicting files** from sync error messages
+2. **Choose consistent naming convention** for your project
+3. **Rename files** to follow the convention
+4. **Re-run sync** to verify resolution
+
+### Bulk Renaming Strategy
+
+For projects with many conflicts:
+
+1. **Backup your project** before making changes
+2. **Standardize on lowercase** file and directory names
+3. **Replace spaces with hyphens** in file names
+4. **Use consistent character encoding** (UTF-8)
+5. **Test sync after each batch** of changes
+
+## System Enhancements
+
+### Recent Improvements (v0.13+)
+
+1. **Enhanced conflict detection** before database operations
+2. **Improved error messages** with specific resolution guidance
+3. **Character normalization utilities** for consistent handling
+4. **File swap detection** for complex move scenarios
+5. **Proactive conflict warnings** during permalink resolution
+
+### Monitoring and Logging
+
+The system now provides detailed logging for conflict resolution:
+
+```
+DEBUG: Detected potential file path conflicts for 'Finance/Investment.md': ['finance/investment.md']
+WARNING: File path conflict detected during move: entity_id=123 trying to move from 'old.md' to 'new.md'
+```
+
+These logs help identify and resolve conflicts before they cause sync failures.
+
+## Support and Resources
+
+If you encounter character-related conflicts not covered in this guide:
+
+1. **Check the logs** for specific conflict details
+2. **Review error messages** for resolution guidance  
+3. **Report issues** with examples of the conflicting files
+4. **Consider the file naming best practices** outlined above
+
+The Basic Memory system is designed to handle most character conflicts automatically while providing clear guidance for manual resolution when needed.

justfile

@@ -3,6 +3,9 @@
 # Install dependencies
 install:
     pip install -e ".[dev]"
+    uv sync
+    @echo ""
+    @echo "💡 Remember to activate the virtual environment by running: source .venv/bin/activate"
 
 # Run unit tests in parallel
 test-unit:
@@ -17,7 +20,7 @@ test: test-unit test-int
 
 # Lint and fix code
 lint:
-    ruff check . --fix
+    uv run ruff check . --fix
 
 # Type check code
 type-check:
@@ -179,4 +182,4 @@ beta version:
 
 # List all available recipes
 default:
-    @just --list
+    @just --list

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 |

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "alembic>=1.14.1",
     "pillow>=11.1.0",
     "pybars3>=0.9.7",
-    "fastmcp>=2.3.4",
+    "fastmcp==2.10.2",
     "pyjwt>=2.10.1",
     "python-dotenv>=1.1.0",
     "pytest-aio>=1.9.0",
@@ -52,7 +52,7 @@ build-backend = "hatchling.build"
 
 [tool.pytest.ini_options]
 pythonpath = ["src", "tests"]
-addopts = "--cov=basic_memory --cov-report term-missing -ra -q"
+addopts = "--cov=basic_memory --cov-report term-missing"
 testpaths = ["tests"]
 asyncio_mode = "strict"
 asyncio_default_fixture_loop_scope = "function"
@@ -123,4 +123,4 @@ omit = [
 ]
 
 [tool.logfire]
-ignore_no_config = true
+ignore_no_config = true

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__ = "0.13.7"
+__version__ = "0.14.4"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

src/basic_memory/alembic/env.py

@@ -8,17 +8,19 @@ from sqlalchemy import pool
 
 from alembic import context
 
+from basic_memory.config import ConfigManager
+
 # set config.env to "test" for pytest to prevent logging to file in utils.setup_logging()
 os.environ["BASIC_MEMORY_ENV"] = "test"
 
 # Import after setting environment variable  # noqa: E402
-from basic_memory.config import app_config  # noqa: E402
 from basic_memory.models import Base  # noqa: E402
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
 config = context.config
 
+app_config = ConfigManager().config
 # Set the SQLAlchemy URL from our app config
 sqlalchemy_url = f"sqlite:///{app_config.database_path}"
 config.set_main_option("sqlalchemy.url", sqlalchemy_url)

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/app.py

@@ -20,15 +20,18 @@ from basic_memory.api.routers import (
     search,
     prompt_router,
 )
-from basic_memory.config import app_config
+from basic_memory.config import ConfigManager
 from basic_memory.services.initialization import initialize_app, initialize_file_sync
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
     """Lifecycle manager for the FastAPI app."""
+
+    app_config = ConfigManager().config
     # Initialize app and database
     logger.info("Starting Basic Memory API")
+    print(f"fastapi {app_config.projects}")
     await initialize_app(app_config)
 
     logger.info(f"Sync changes enabled: {app_config.sync_changes}")

src/basic_memory/api/routers/management_router.py

@@ -6,7 +6,7 @@ from fastapi import APIRouter, Request
 from loguru import logger
 from pydantic import BaseModel
 
-from basic_memory.config import app_config
+from basic_memory.config import ConfigManager
 from basic_memory.deps import SyncServiceDep, ProjectRepositoryDep
 
 router = APIRouter(prefix="/management", tags=["management"])
@@ -41,6 +41,8 @@ async def start_watch_service(
         # Watch service is already running
         return WatchStatusResponse(running=True)
 
+    app_config = ConfigManager().config
+
     # Create and start a new watch service
     logger.info("Starting watch service via management API")
 

src/basic_memory/api/routers/project_router.py

@@ -1,5 +1,6 @@
 """Router for project management."""
 
+import os
 from fastapi import APIRouter, HTTPException, Path, Body
 from typing import Optional
 
@@ -32,40 +33,47 @@ async def get_project_info(
 @project_router.patch("/{name}", response_model=ProjectStatusResponse)
 async def update_project(
     project_service: ProjectServiceDep,
-    project_name: str = Path(..., description="Name of the project to update"),
-    path: Optional[str] = Body(None, description="New path for the project"),
+    name: str = Path(..., description="Name of the project to update"),
+    path: Optional[str] = Body(None, description="New absolute path for the project"),
     is_active: Optional[bool] = Body(None, description="Status of the project (active/inactive)"),
 ) -> ProjectStatusResponse:
     """Update a project's information in configuration and database.
 
     Args:
-        project_name: The name of the project to update
-        path: Optional new path for the project
+        name: The name of the project to update
+        path: Optional new absolute path for the project
         is_active: Optional status update for the project
 
     Returns:
         Response confirming the project was updated
     """
-    try:  # pragma: no cover
+    try:
+        # Validate that path is absolute if provided
+        if path and not os.path.isabs(path):
+            raise HTTPException(status_code=400, detail="Path must be absolute")
+
         # Get original project info for the response
         old_project_info = ProjectItem(
-            name=project_name,
-            path=project_service.projects.get(project_name, ""),
+            name=name,
+            path=project_service.projects.get(name, ""),
         )
 
-        await project_service.update_project(project_name, updated_path=path, is_active=is_active)
+        if path:
+            await project_service.move_project(name, path)
+        elif is_active is not None:
+            await project_service.update_project(name, is_active=is_active)
 
         # Get updated project info
-        updated_path = path if path else project_service.projects.get(project_name, "")
+        updated_path = path if path else project_service.projects.get(name, "")
 
         return ProjectStatusResponse(
-            message=f"Project '{project_name}' updated successfully",
+            message=f"Project '{name}' updated successfully",
             status="success",
-            default=(project_name == project_service.default_project),
+            default=(name == project_service.default_project),
             old_project=old_project_info,
-            new_project=ProjectItem(name=project_name, path=updated_path),
+            new_project=ProjectItem(name=name, path=updated_path),
         )
-    except ValueError as e:  # pragma: no cover
+    except ValueError as e:
         raise HTTPException(status_code=400, detail=str(e))
 
 

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/api/routers/utils.py

@@ -52,7 +52,7 @@ async def to_graph_context(
                     file_path=item.file_path,
                     permalink=item.permalink,  # pyright: ignore
                     relation_type=item.relation_type,  # pyright: ignore
-                    from_entity=from_entity.title,  # pyright: ignore
+                    from_entity=from_entity.title if from_entity else None,
                     to_entity=to_entity.title if to_entity else None,
                     created_at=item.created_at,
                 )

src/basic_memory/cli/app.py

@@ -2,7 +2,7 @@ from typing import Optional
 
 import typer
 
-from basic_memory.config import get_project_config
+from basic_memory.config import get_project_config, ConfigManager
 from basic_memory.mcp.project_session import session
 
 
@@ -10,8 +10,8 @@ def version_callback(value: bool) -> None:
     """Show version and exit."""
     if value:  # pragma: no cover
         import basic_memory
-        from basic_memory.config import config
 
+        config = get_project_config()
         typer.echo(f"Basic Memory version: {basic_memory.__version__}")
         typer.echo(f"Current project: {config.project}")
         typer.echo(f"Project path: {config.home}")
@@ -44,9 +44,9 @@ def app_callback(
 
     # Run initialization for every command unless --version was specified
     if not version and ctx.invoked_subcommand is not None:
-        from basic_memory.config import app_config
         from basic_memory.services.initialization import ensure_initialization
 
+        app_config = ConfigManager().config
         ensure_initialization(app_config)
 
         # Initialize MCP session with the specified project or default

src/basic_memory/cli/commands/__init__.py

@@ -1,10 +1,9 @@
 """CLI commands for basic-memory."""
 
-from . import auth, status, sync, db, import_memory_json, mcp, import_claude_conversations
+from . import status, sync, db, import_memory_json, mcp, import_claude_conversations
 from . import import_claude_projects, import_chatgpt, tool, project
 
 __all__ = [
-    "auth",
     "status",
     "sync",
     "db",

src/basic_memory/cli/commands/auth.py

@@ -1,136 +0,0 @@
-"""OAuth management commands."""
-
-import typer
-from typing import Optional
-from pydantic import AnyHttpUrl
-
-from basic_memory.cli.app import app
-from basic_memory.mcp.auth_provider import BasicMemoryOAuthProvider
-from mcp.shared.auth import OAuthClientInformationFull
-
-
-auth_app = typer.Typer(help="OAuth client management commands")
-app.add_typer(auth_app, name="auth")
-
-
-@auth_app.command()
-def register_client(
-    client_id: Optional[str] = typer.Option(
-        None, help="Client ID (auto-generated if not provided)"
-    ),
-    client_secret: Optional[str] = typer.Option(
-        None, help="Client secret (auto-generated if not provided)"
-    ),
-    issuer_url: str = typer.Option("http://localhost:8000", help="OAuth issuer URL"),
-):
-    """Register a new OAuth client for Basic Memory MCP server."""
-
-    # Create provider instance
-    provider = BasicMemoryOAuthProvider(issuer_url=issuer_url)
-
-    # Create client info with required redirect_uris
-    client_info = OAuthClientInformationFull(
-        client_id=client_id or "",  # Provider will generate if empty
-        client_secret=client_secret or "",  # Provider will generate if empty
-        redirect_uris=[AnyHttpUrl("http://localhost:8000/callback")],  # Default redirect URI
-        client_name="Basic Memory OAuth Client",
-        grant_types=["authorization_code", "refresh_token"],
-    )
-
-    # Register the client
-    import asyncio
-
-    asyncio.run(provider.register_client(client_info))
-
-    typer.echo("Client registered successfully!")
-    typer.echo(f"Client ID: {client_info.client_id}")
-    typer.echo(f"Client Secret: {client_info.client_secret}")
-    typer.echo("\nSave these credentials securely - the client secret cannot be retrieved later.")
-
-
-@auth_app.command()
-def test_auth(
-    issuer_url: str = typer.Option("http://localhost:8000", help="OAuth issuer URL"),
-):
-    """Test OAuth authentication flow.
-
-    IMPORTANT: Use the same FASTMCP_AUTH_SECRET_KEY environment variable
-    as your MCP server for tokens to validate correctly.
-    """
-
-    import asyncio
-    import secrets
-    from mcp.server.auth.provider import AuthorizationParams
-    from pydantic import AnyHttpUrl
-
-    async def test_flow():
-        # Create provider with same secret key as server
-        provider = BasicMemoryOAuthProvider(issuer_url=issuer_url)
-
-        # Register a test client
-        client_info = OAuthClientInformationFull(
-            client_id=secrets.token_urlsafe(16),
-            client_secret=secrets.token_urlsafe(32),
-            redirect_uris=[AnyHttpUrl("http://localhost:8000/callback")],
-            client_name="Test OAuth Client",
-            grant_types=["authorization_code", "refresh_token"],
-        )
-        await provider.register_client(client_info)
-        typer.echo(f"Registered test client: {client_info.client_id}")
-
-        # Get the client
-        client = await provider.get_client(client_info.client_id)
-        if not client:
-            typer.echo("Error: Client not found after registration", err=True)
-            return
-
-        # Create authorization request
-        auth_params = AuthorizationParams(
-            state="test-state",
-            scopes=["read", "write"],
-            code_challenge="test-challenge",
-            redirect_uri=AnyHttpUrl("http://localhost:8000/callback"),
-            redirect_uri_provided_explicitly=True,
-        )
-
-        # Get authorization URL
-        auth_url = await provider.authorize(client, auth_params)
-        typer.echo(f"Authorization URL: {auth_url}")
-
-        # Extract auth code from URL
-        from urllib.parse import urlparse, parse_qs
-
-        parsed = urlparse(auth_url)
-        params = parse_qs(parsed.query)
-        auth_code = params.get("code", [None])[0]
-
-        if not auth_code:
-            typer.echo("Error: No authorization code in URL", err=True)
-            return
-
-        # Load the authorization code
-        code_obj = await provider.load_authorization_code(client, auth_code)
-        if not code_obj:
-            typer.echo("Error: Invalid authorization code", err=True)
-            return
-
-        # Exchange for tokens
-        token = await provider.exchange_authorization_code(client, code_obj)
-        typer.echo(f"Access token: {token.access_token}")
-        typer.echo(f"Refresh token: {token.refresh_token}")
-        typer.echo(f"Expires in: {token.expires_in} seconds")
-
-        # Validate access token
-        access_token_obj = await provider.load_access_token(token.access_token)
-        if access_token_obj:
-            typer.echo("Access token validated successfully!")
-            typer.echo(f"Client ID: {access_token_obj.client_id}")
-            typer.echo(f"Scopes: {access_token_obj.scopes}")
-        else:
-            typer.echo("Error: Invalid access token", err=True)
-
-    asyncio.run(test_flow())
-
-
-if __name__ == "__main__":
-    auth_app()

src/basic_memory/cli/commands/db.py

@@ -1,14 +1,13 @@
 """Database management commands."""
 
 import asyncio
-from pathlib import Path
 
 import typer
 from loguru import logger
 
 from basic_memory import db
 from basic_memory.cli.app import app
-from basic_memory.config import app_config, config_manager
+from basic_memory.config import ConfigManager, BasicMemoryConfig, save_basic_memory_config
 
 
 @app.command()
@@ -18,6 +17,8 @@ def reset(
     """Reset database (drop all tables and recreate)."""
     if typer.confirm("This will delete all data in your db. Are you sure?"):
         logger.info("Resetting database...")
+        config_manager = ConfigManager()
+        app_config = config_manager.config
         # Get database path
         db_path = app_config.app_database_path
 
@@ -27,9 +28,8 @@ def reset(
             logger.info(f"Database file deleted: {db_path}")
 
         # Reset project configuration
-        config_manager.config.projects = {"main": str(Path.home() / "basic-memory")}
-        config_manager.config.default_project = "main"
-        config_manager.save_config(config_manager.config)
+        config = BasicMemoryConfig()
+        save_basic_memory_config(config_manager.config_file, config)
         logger.info("Project configuration reset to default")
 
         # Create a new empty database

src/basic_memory/cli/commands/import_chatgpt.py

@@ -7,7 +7,7 @@ from typing import Annotated
 
 import typer
 from basic_memory.cli.app import import_app
-from basic_memory.config import config
+from basic_memory.config import get_project_config
 from basic_memory.importers import ChatGPTImporter
 from basic_memory.markdown import EntityParser, MarkdownProcessor
 from loguru import logger
@@ -19,6 +19,7 @@ console = Console()
 
 async def get_markdown_processor() -> MarkdownProcessor:
     """Get MarkdownProcessor instance."""
+    config = get_project_config()
     entity_parser = EntityParser(config.home)
     return MarkdownProcessor(entity_parser)
 
@@ -49,7 +50,7 @@ def import_chatgpt(
 
         # Get markdown processor
         markdown_processor = asyncio.run(get_markdown_processor())
-
+        config = get_project_config()
         # Process the file
         base_path = config.home / folder
         console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -7,7 +7,7 @@ from typing import Annotated
 
 import typer
 from basic_memory.cli.app import claude_app
-from basic_memory.config import config
+from basic_memory.config import get_project_config
 from basic_memory.importers.claude_conversations_importer import ClaudeConversationsImporter
 from basic_memory.markdown import EntityParser, MarkdownProcessor
 from loguru import logger
@@ -19,6 +19,7 @@ console = Console()
 
 async def get_markdown_processor() -> MarkdownProcessor:
     """Get MarkdownProcessor instance."""
+    config = get_project_config()
     entity_parser = EntityParser(config.home)
     return MarkdownProcessor(entity_parser)
 
@@ -42,6 +43,7 @@ def import_claude(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
+    config = get_project_config()
     try:
         if not conversations_json.exists():
             typer.echo(f"Error: File not found: {conversations_json}", err=True)

src/basic_memory/cli/commands/import_claude_projects.py

@@ -7,7 +7,7 @@ from typing import Annotated
 
 import typer
 from basic_memory.cli.app import claude_app
-from basic_memory.config import config
+from basic_memory.config import get_project_config
 from basic_memory.importers.claude_projects_importer import ClaudeProjectsImporter
 from basic_memory.markdown import EntityParser, MarkdownProcessor
 from loguru import logger
@@ -19,6 +19,7 @@ console = Console()
 
 async def get_markdown_processor() -> MarkdownProcessor:
     """Get MarkdownProcessor instance."""
+    config = get_project_config()
     entity_parser = EntityParser(config.home)
     return MarkdownProcessor(entity_parser)
 
@@ -41,6 +42,7 @@ def import_projects(
 
     After importing, run 'basic-memory sync' to index the new files.
     """
+    config = get_project_config()
     try:
         if not projects_json.exists():
             typer.echo(f"Error: File not found: {projects_json}", err=True)

src/basic_memory/cli/commands/import_memory_json.py

@@ -7,7 +7,7 @@ from typing import Annotated
 
 import typer
 from basic_memory.cli.app import import_app
-from basic_memory.config import config
+from basic_memory.config import get_project_config
 from basic_memory.importers.memory_json_importer import MemoryJsonImporter
 from basic_memory.markdown import EntityParser, MarkdownProcessor
 from loguru import logger
@@ -19,6 +19,7 @@ console = Console()
 
 async def get_markdown_processor() -> MarkdownProcessor:
     """Get MarkdownProcessor instance."""
+    config = get_project_config()
     entity_parser = EntityParser(config.home)
     return MarkdownProcessor(entity_parser)
 
@@ -46,6 +47,7 @@ def memory_json(
         typer.echo(f"Error: File not found: {json_path}", err=True)
         raise typer.Exit(1)
 
+    config = get_project_config()
     try:
         # Get markdown processor
         markdown_processor = asyncio.run(get_markdown_processor())
@@ -74,7 +76,8 @@ def memory_json(
             Panel(
                 f"[green]Import complete![/green]\n\n"
                 f"Created {result.entities} entities\n"
-                f"Added {result.relations} relations",
+                f"Added {result.relations} relations\n"
+                f"Skipped {result.skipped_entities} entities\n",
                 expand=False,
             )
         )

src/basic_memory/cli/commands/mcp.py

@@ -4,6 +4,7 @@ import asyncio
 import typer
 
 from basic_memory.cli.app import app
+from basic_memory.config import ConfigManager
 
 # Import mcp instance
 from basic_memory.mcp.server import mcp as mcp_server  # pragma: no cover
@@ -34,26 +35,13 @@ def mcp(
     - sse: Server-Sent Events (for compatibility with existing clients)
     """
 
-    # Check if OAuth is enabled
-    import os
-
-    auth_enabled = os.getenv("FASTMCP_AUTH_ENABLED", "false").lower() == "true"
-    if auth_enabled:
-        logger.info("OAuth authentication is ENABLED")
-        logger.info(f"Issuer URL: {os.getenv('FASTMCP_AUTH_ISSUER_URL', 'http://localhost:8000')}")
-        if os.getenv("FASTMCP_AUTH_REQUIRED_SCOPES"):
-            logger.info(f"Required scopes: {os.getenv('FASTMCP_AUTH_REQUIRED_SCOPES')}")
-    else:
-        logger.info("OAuth authentication is DISABLED")
-
-    from basic_memory.config import app_config
     from basic_memory.services.initialization import initialize_file_sync
 
-    # Start the MCP server with the specified transport
-
     # Use unified thread-based sync approach for both transports
     import threading
 
+    app_config = ConfigManager().config
+
     def run_file_sync():
         """Run file sync in a separate thread with its own event loop."""
         loop = asyncio.new_event_loop()
@@ -78,7 +66,6 @@ def mcp(
     if transport == "stdio":
         mcp_server.run(
             transport=transport,
-            log_level="INFO",
         )
     elif transport == "streamable-http" or transport == "sse":
         mcp_server.run(

src/basic_memory/cli/commands/project.py

@@ -24,6 +24,7 @@ from basic_memory.schemas.project_info import ProjectStatusResponse
 from basic_memory.mcp.tools.utils import call_delete
 from basic_memory.mcp.tools.utils import call_put
 from basic_memory.utils import generate_permalink
+from basic_memory.mcp.tools.utils import call_patch
 
 console = Console()
 
@@ -73,7 +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}
@@ -99,8 +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]")
@@ -118,9 +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]")
@@ -148,6 +148,46 @@ def synchronize_projects() -> None:
         raise typer.Exit(1)
 
 
+@project_app.command("move")
+def move_project(
+    name: str = typer.Argument(..., help="Name of the project to move"),
+    new_path: str = typer.Argument(..., help="New absolute path for the project"),
+) -> None:
+    """Move a project to a new location."""
+    # Resolve to absolute path
+    resolved_path = Path(os.path.abspath(os.path.expanduser(new_path))).as_posix()
+
+    try:
+        data = {"path": resolved_path}
+
+        project_permalink = generate_permalink(name)
+        current_project = session.get_current_project()
+        response = asyncio.run(
+            call_patch(client, f"/{current_project}/project/{project_permalink}", json=data)
+        )
+        result = ProjectStatusResponse.model_validate(response.json())
+
+        console.print(f"[green]{result.message}[/green]")
+
+        # Show important file movement reminder
+        console.print()  # Empty line for spacing
+        console.print(
+            Panel(
+                "[bold red]IMPORTANT:[/bold red] Project configuration updated successfully.\n\n"
+                "[yellow]You must manually move your project files from the old location to:[/yellow]\n"
+                f"[cyan]{resolved_path}[/cyan]\n\n"
+                "[dim]Basic Memory has only updated the configuration - your files remain in their original location.[/dim]",
+                title="⚠️  Manual File Movement Required",
+                border_style="yellow",
+                expand=False,
+            )
+        )
+
+    except Exception as e:
+        console.print(f"[red]Error moving project: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
 @project_app.command("info")
 def display_project_info(
     json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),

src/basic_memory/cli/commands/status.py

@@ -12,7 +12,7 @@ from rich.tree import Tree
 from basic_memory import db
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.sync import get_sync_service
-from basic_memory.config import config, app_config
+from basic_memory.config import ConfigManager, get_project_config
 from basic_memory.repository import ProjectRepository
 from basic_memory.sync.sync_service import SyncReport
 
@@ -126,6 +126,9 @@ async def run_status(verbose: bool = False):  # pragma: no cover
     """Check sync status of files vs database."""
     # Check knowledge/ directory
 
+    app_config = ConfigManager().config
+    config = get_project_config()
+
     _, session_maker = await db.get_or_create_db(
         db_path=app_config.database_path, db_type=db.DatabaseType.FILESYSTEM
     )

src/basic_memory/cli/commands/sync.py

@@ -13,7 +13,7 @@ from rich.tree import Tree
 
 from basic_memory import db
 from basic_memory.cli.app import app
-from basic_memory.config import config
+from basic_memory.config import ConfigManager, get_project_config
 from basic_memory.markdown import EntityParser
 from basic_memory.markdown.markdown_processor import MarkdownProcessor
 from basic_memory.models import Project
@@ -29,7 +29,6 @@ from basic_memory.services.link_resolver import LinkResolver
 from basic_memory.services.search_service import SearchService
 from basic_memory.sync import SyncService
 from basic_memory.sync.sync_service import SyncReport
-from basic_memory.config import app_config
 
 console = Console()
 
@@ -42,6 +41,8 @@ class ValidationIssue:
 
 async def get_sync_service(project: Project) -> SyncService:  # pragma: no cover
     """Get sync service instance with all dependencies."""
+
+    app_config = ConfigManager().config
     _, session_maker = await db.get_or_create_db(
         db_path=app_config.database_path, db_type=db.DatabaseType.FILESYSTEM
     )
@@ -96,6 +97,7 @@ def group_issues_by_directory(issues: List[ValidationIssue]) -> Dict[str, List[V
 
 def display_sync_summary(knowledge: SyncReport):
     """Display a one-line summary of sync changes."""
+    config = get_project_config()
     total_changes = knowledge.total
     project_name = config.project
 
@@ -124,6 +126,7 @@ def display_sync_summary(knowledge: SyncReport):
 
 def display_detailed_sync_results(knowledge: SyncReport):
     """Display detailed sync results with trees."""
+    config = get_project_config()
     project_name = config.project
 
     if knowledge.total == 0:
@@ -158,6 +161,9 @@ def display_detailed_sync_results(knowledge: SyncReport):
 
 async def run_sync(verbose: bool = False):
     """Run sync operation."""
+    app_config = ConfigManager().config
+    config = get_project_config()
+
     _, session_maker = await db.get_or_create_db(
         db_path=app_config.database_path, db_type=db.DatabaseType.FILESYSTEM
     )
@@ -212,6 +218,8 @@ def sync(
     ),
 ) -> None:
     """Sync knowledge files with the database."""
+    config = get_project_config()
+
     try:
         # Show which project we're syncing
         typer.echo(f"Syncing project: {config.project}")

src/basic_memory/cli/main.py

@@ -4,7 +4,6 @@ from basic_memory.cli.app import app  # pragma: no cover
 
 # Register commands
 from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
-    auth,
     db,
     import_chatgpt,
     import_claude_conversations,

src/basic_memory/config.py

@@ -45,7 +45,9 @@ class BasicMemoryConfig(BaseSettings):
     env: Environment = Field(default="dev", description="Environment name")
 
     projects: Dict[str, str] = Field(
-        default_factory=lambda: {"main": str(Path.home() / "basic-memory")},
+        default_factory=lambda: {
+            "main": Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")).as_posix()
+        },
         description="Mapping of project names to their filesystem paths",
     )
     default_project: str = Field(
@@ -72,6 +74,17 @@ 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,
+        description="URL of remote Basic Memory API. If set, MCP will connect to this API instead of using local ASGI transport.",
+    )
+
     model_config = SettingsConfigDict(
         env_prefix="BASIC_MEMORY_",
         extra="ignore",
@@ -92,7 +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(Path.home() / "basic-memory")
+            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
@@ -120,6 +135,7 @@ class BasicMemoryConfig(BaseSettings):
         """
 
         # Load the app-level database path from the global config
+        config_manager = ConfigManager()
         config = config_manager.load_config()  # pragma: no cover
         return config.app_database_path  # pragma: no cover
 
@@ -158,20 +174,21 @@ class ConfigManager:
         # Ensure config directory exists
         self.config_dir.mkdir(parents=True, exist_ok=True)
 
-        # Load or create configuration
-        self.config = self.load_config()
+    @property
+    def config(self) -> BasicMemoryConfig:
+        """Get configuration, loading it lazily if needed."""
+        return self.load_config()
 
     def load_config(self) -> BasicMemoryConfig:
         """Load configuration from file or create default."""
+
         if self.config_file.exists():
             try:
                 data = json.loads(self.config_file.read_text(encoding="utf-8"))
                 return BasicMemoryConfig(**data)
             except Exception as e:  # pragma: no cover
-                logger.error(f"Failed to load config: {e}")
-                config = BasicMemoryConfig()
-                self.save_config(config)
-                return config
+                logger.exception(f"Failed to load config: {e}")
+                raise e
         else:
             config = BasicMemoryConfig()
             self.save_config(config)
@@ -179,10 +196,7 @@ class ConfigManager:
 
     def save_config(self, config: BasicMemoryConfig) -> None:
         """Save configuration to file."""
-        try:
-            self.config_file.write_text(json.dumps(config.model_dump(), indent=2))
-        except Exception as e:  # pragma: no cover
-            logger.error(f"Failed to save config: {e}")
+        save_basic_memory_config(self.config_file, config)
 
     @property
     def projects(self) -> Dict[str, str]:
@@ -204,8 +218,10 @@ class ConfigManager:
         project_path = Path(path)
         project_path.mkdir(parents=True, exist_ok=True)  # pragma: no cover
 
-        self.config.projects[name] = str(project_path)
-        self.save_config(self.config)
+        # Load config, modify it, and save it
+        config = self.load_config()
+        config.projects[name] = project_path.as_posix()
+        self.save_config(config)
         return ProjectConfig(name=name, home=project_path)
 
     def remove_project(self, name: str) -> None:
@@ -215,11 +231,13 @@ class ConfigManager:
         if not project_name:  # pragma: no cover
             raise ValueError(f"Project '{name}' not found")
 
-        if project_name == self.config.default_project:  # pragma: no cover
+        # Load config, check, modify, and save
+        config = self.load_config()
+        if project_name == config.default_project:  # pragma: no cover
             raise ValueError(f"Cannot remove the default project '{name}'")
 
-        del self.config.projects[name]
-        self.save_config(self.config)
+        del config.projects[name]
+        self.save_config(config)
 
     def set_default_project(self, name: str) -> None:
         """Set the default project."""
@@ -227,15 +245,18 @@ class ConfigManager:
         if not project_name:  # pragma: no cover
             raise ValueError(f"Project '{name}' not found")
 
-        self.config.default_project = name
-        self.save_config(self.config)
+        # Load config, modify, and save
+        config = self.load_config()
+        config.default_project = project_name
+        self.save_config(config)
 
     def get_project(self, name: str) -> Tuple[str, str] | Tuple[None, None]:
         """Look up a project from the configuration by name or permalink"""
         project_permalink = generate_permalink(name)
-        for name, path in app_config.projects.items():
-            if project_permalink == generate_permalink(name):
-                return name, path
+        app_config = self.config
+        for project_name, path in app_config.projects.items():
+            if project_permalink == generate_permalink(project_name):
+                return project_name, path
         return None, None
 
 
@@ -248,7 +269,7 @@ def get_project_config(project_name: Optional[str] = None) -> ProjectConfig:
     actual_project_name = None
 
     # load the config from file
-    global app_config
+    config_manager = ConfigManager()
     app_config = config_manager.load_config()
 
     # Get project name from environment variable
@@ -278,14 +299,12 @@ def get_project_config(project_name: Optional[str] = None) -> ProjectConfig:
     raise ValueError(f"Project '{actual_project_name}' not found")  # pragma: no cover
 
 
-# Create config manager
-config_manager = ConfigManager()
-
-# Export the app-level config
-app_config: BasicMemoryConfig = config_manager.config
-
-# Load project config for the default project (backward compatibility)
-config: ProjectConfig = get_project_config()
+def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None:
+    """Save configuration to file."""
+    try:
+        file_path.write_text(json.dumps(config.model_dump(), indent=2))
+    except Exception as e:  # pragma: no cover
+        logger.error(f"Failed to save config: {e}")
 
 
 def update_current_project(project_name: str) -> None:
@@ -337,12 +356,24 @@ def setup_basic_memory_logging():  # pragma: no cover
         # print("Skipping duplicate logging setup")
         return
 
+    # 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.load_config().log_level,
+        log_level=log_level,
         log_file=f"{DATA_DIR_NAME}/basic-memory-{process_name}.log",
-        console=False,
+        console=console_logging,
     )
 
     logger.info(f"Basic Memory {basic_memory.__version__} (Project: {config.project})")

src/basic_memory/db.py

@@ -4,7 +4,7 @@ from enum import Enum, auto
 from pathlib import Path
 from typing import AsyncGenerator, Optional
 
-from basic_memory.config import BasicMemoryConfig
+from basic_memory.config import BasicMemoryConfig, ConfigManager
 from alembic import command
 from alembic.config import Config
 
@@ -88,7 +88,6 @@ async def get_or_create_db(
     db_path: Path,
     db_type: DatabaseType = DatabaseType.FILESYSTEM,
     ensure_migrations: bool = True,
-    app_config: Optional["BasicMemoryConfig"] = None,
 ) -> tuple[AsyncEngine, async_sessionmaker[AsyncSession]]:  # pragma: no cover
     """Get or create database engine and session maker."""
     global _engine, _session_maker
@@ -98,10 +97,7 @@ async def get_or_create_db(
 
         # Run migrations automatically unless explicitly disabled
         if ensure_migrations:
-            if app_config is None:
-                from basic_memory.config import app_config as global_app_config
-
-                app_config = global_app_config
+            app_config = ConfigManager().config
             await run_migrations(app_config, db_type)
 
     # These checks should never fail since we just created the engine and session maker

src/basic_memory/deps.py

@@ -12,7 +12,7 @@ from sqlalchemy.ext.asyncio import (
 import pathlib
 
 from basic_memory import db
-from basic_memory.config import ProjectConfig, BasicMemoryConfig
+from basic_memory.config import ProjectConfig, BasicMemoryConfig, ConfigManager
 from basic_memory.importers import (
     ChatGPTImporter,
     ClaudeConversationsImporter,
@@ -33,10 +33,10 @@ from basic_memory.services.file_service import FileService
 from basic_memory.services.link_resolver import LinkResolver
 from basic_memory.services.search_service import SearchService
 from basic_memory.sync import SyncService
-from basic_memory.config import app_config
 
 
 def get_app_config() -> BasicMemoryConfig:  # pragma: no cover
+    app_config = ConfigManager().config
     return app_config
 
 
@@ -297,6 +297,7 @@ ContextServiceDep = Annotated[ContextService, Depends(get_context_service)]
 
 
 async def get_sync_service(
+    app_config: AppConfigDep,
     entity_service: EntityServiceDep,
     entity_parser: EntityParserDep,
     entity_repository: EntityRepositoryDep,

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
@@ -193,7 +193,7 @@ class ChatGPTImporter(Importer[ChatImportResult]):
     def _traverse_messages(
         self, mapping: Dict[str, Any], root_id: Optional[str], seen: Set[str]
     ) -> List[Dict[str, Any]]:  # pragma: no cover
-        """Traverse message tree and return messages in order.
+        """Traverse message tree iteratively to handle deep conversations.
 
         Args:
             mapping: Message mapping.
@@ -204,19 +204,29 @@ class ChatGPTImporter(Importer[ChatImportResult]):
             List of message data.
         """
         messages = []
-        node = mapping.get(root_id) if root_id else None
+        if not root_id:
+            return messages
 
-        while node:
+        # Use iterative approach with stack to avoid recursion depth issues
+        stack = [root_id]
+
+        while stack:
+            node_id = stack.pop()
+            if not node_id:
+                continue
+
+            node = mapping.get(node_id)
+            if not node:
+                continue
+
+            # Process current node if it has a message and hasn't been seen
             if node["id"] not in seen and node.get("message"):
                 seen.add(node["id"])
                 messages.append(node["message"])
 
-            # Follow children
+            # Add children to stack in reverse order to maintain conversation flow
             children = node.get("children", [])
-            for child_id in children:
-                child_msgs = self._traverse_messages(mapping, child_id, seen)
-                messages.extend(child_msgs)
-
-            break  # Don't follow siblings
+            for child_id in reversed(children):
+                stack.append(child_id)
 
         return messages

src/basic_memory/importers/memory_json_importer.py

@@ -3,7 +3,7 @@
 import logging
 from typing import Any, Dict, List
 
-from basic_memory.config import config
+from basic_memory.config import get_project_config
 from basic_memory.markdown.schemas import EntityFrontmatter, EntityMarkdown, Observation, Relation
 from basic_memory.importers.base import Importer
 from basic_memory.schemas.importer import EntityImportResult
@@ -27,10 +27,12 @@ class MemoryJsonImporter(Importer[EntityImportResult]):
         Returns:
             EntityImportResult containing statistics and status of the import.
         """
+        config = get_project_config()
         try:
             # First pass - collect all relations by source entity
             entity_relations: Dict[str, List[Relation]] = {}
             entities: Dict[str, Dict[str, Any]] = {}
+            skipped_entities: int = 0
 
             # Ensure the base path exists
             base_path = config.home  # pragma: no cover
@@ -41,7 +43,13 @@ class MemoryJsonImporter(Importer[EntityImportResult]):
             for line in source_data:
                 data = line
                 if data["type"] == "entity":
-                    entities[data["name"]] = data
+                    # Handle different possible name keys
+                    entity_name = data.get("name") or data.get("entityName") or data.get("id")
+                    if not entity_name:
+                        logger.warning(f"Entity missing name field: {data}")
+                        skipped_entities += 1
+                        continue
+                    entities[entity_name] = data
                 elif data["type"] == "relation":
                     # Store relation with its source entity
                     source = data.get("from") or data.get("from_id")
@@ -57,25 +65,31 @@ class MemoryJsonImporter(Importer[EntityImportResult]):
             # Second pass - create and write entities
             entities_created = 0
             for name, entity_data in entities.items():
+                # Get entity type with fallback
+                entity_type = entity_data.get("entityType") or entity_data.get("type") or "entity"
+
                 # Ensure entity type directory exists
-                entity_type_dir = base_path / entity_data["entityType"]
+                entity_type_dir = base_path / entity_type
                 entity_type_dir.mkdir(parents=True, exist_ok=True)
 
+                # Get observations with fallback to empty list
+                observations = entity_data.get("observations", [])
+
                 entity = EntityMarkdown(
                     frontmatter=EntityFrontmatter(
                         metadata={
-                            "type": entity_data["entityType"],
+                            "type": entity_type,
                             "title": name,
-                            "permalink": f"{entity_data['entityType']}/{name}",
+                            "permalink": f"{entity_type}/{name}",
                         }
                     ),
                     content=f"# {name}\n",
-                    observations=[Observation(content=obs) for obs in entity_data["observations"]],
+                    observations=[Observation(content=obs) for obs in observations],
                     relations=entity_relations.get(name, []),
                 )
 
                 # Write entity file
-                file_path = base_path / f"{entity_data['entityType']}/{name}.md"
+                file_path = base_path / f"{entity_type}/{name}.md"
                 await self.write_entity(entity, file_path)
                 entities_created += 1
 
@@ -86,6 +100,7 @@ class MemoryJsonImporter(Importer[EntityImportResult]):
                 success=True,
                 entities=entities_created,
                 relations=relations_count,
+                skipped_entities=skipped_entities,
             )
 
         except Exception as e:  # pragma: no cover

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

@@ -38,8 +38,10 @@ def entity_model_from_markdown(
     # Update basic fields
     model.title = markdown.frontmatter.title
     model.entity_type = markdown.frontmatter.type
-    model.permalink = markdown.frontmatter.permalink
-    model.file_path = str(file_path)
+    # 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 = file_path.as_posix()
     model.content_type = "text/markdown"
     model.created_at = markdown.created
     model.updated_at = markdown.modified

src/basic_memory/mcp/async_client.py

@@ -1,8 +1,28 @@
 from httpx import ASGITransport, AsyncClient
+from loguru import logger
 
 from basic_memory.api.app import app as fastapi_app
+from basic_memory.config import ConfigManager
+
+
+def create_client() -> AsyncClient:
+    """Create an HTTP client based on configuration.
+
+    Returns:
+        AsyncClient configured for either local ASGI or remote HTTP transport
+    """
+    config_manager = ConfigManager()
+    config = config_manager.load_config()
+
+    if config.api_url:
+        # Use HTTP transport for remote API
+        logger.info(f"Creating HTTP client for remote Basic Memory API: {config.api_url}")
+        return AsyncClient(base_url=config.api_url)
+    else:
+        # Use ASGI transport for local API
+        logger.debug("Creating ASGI client for local Basic Memory API")
+        return AsyncClient(transport=ASGITransport(app=fastapi_app), base_url="http://test")
 
-BASE_URL = "http://test"
 
 # Create shared async client
-client = AsyncClient(transport=ASGITransport(app=fastapi_app), base_url=BASE_URL)
+client = create_client()

src/basic_memory/mcp/auth_provider.py

@@ -1,270 +0,0 @@
-"""OAuth authentication provider for Basic Memory MCP server."""
-
-import secrets
-from datetime import datetime, timedelta
-from typing import Dict, Optional
-
-import jwt
-from mcp.server.auth.provider import (
-    OAuthAuthorizationServerProvider,
-    AuthorizationParams,
-    AuthorizationCode,
-    RefreshToken,
-    AccessToken,
-)
-from mcp.shared.auth import OAuthClientInformationFull, OAuthToken
-from loguru import logger
-
-
-class BasicMemoryAuthorizationCode(AuthorizationCode):
-    """Extended authorization code with additional metadata."""
-
-    issuer_state: Optional[str] = None
-
-
-class BasicMemoryRefreshToken(RefreshToken):
-    """Extended refresh token with additional metadata."""
-
-    pass
-
-
-class BasicMemoryAccessToken(AccessToken):
-    """Extended access token with additional metadata."""
-
-    pass
-
-
-class BasicMemoryOAuthProvider(
-    OAuthAuthorizationServerProvider[
-        BasicMemoryAuthorizationCode, BasicMemoryRefreshToken, BasicMemoryAccessToken
-    ]
-):
-    """OAuth provider for Basic Memory MCP server.
-
-    This is a simple in-memory implementation that can be extended
-    to integrate with external OAuth providers or use persistent storage.
-    """
-
-    def __init__(self, issuer_url: str = "http://localhost:8000", secret_key: Optional[str] = None):
-        self.issuer_url = issuer_url
-        # Use environment variable for secret key if available, otherwise generate
-        import os
-
-        self.secret_key = (
-            secret_key or os.getenv("FASTMCP_AUTH_SECRET_KEY") or secrets.token_urlsafe(32)
-        )
-
-        # In-memory storage - in production, use a proper database
-        self.clients: Dict[str, OAuthClientInformationFull] = {}
-        self.authorization_codes: Dict[str, BasicMemoryAuthorizationCode] = {}
-        self.refresh_tokens: Dict[str, BasicMemoryRefreshToken] = {}
-        self.access_tokens: Dict[str, BasicMemoryAccessToken] = {}
-
-    async def get_client(self, client_id: str) -> Optional[OAuthClientInformationFull]:
-        """Get a client by ID."""
-        return self.clients.get(client_id)
-
-    async def register_client(self, client_info: OAuthClientInformationFull) -> None:
-        """Register a new OAuth client."""
-        # Generate client ID if not provided
-        if not client_info.client_id:
-            client_info.client_id = secrets.token_urlsafe(16)
-
-        # Generate client secret if not provided
-        if not client_info.client_secret:
-            client_info.client_secret = secrets.token_urlsafe(32)
-
-        self.clients[client_info.client_id] = client_info
-        logger.info(f"Registered OAuth client: {client_info.client_id}")
-
-    async def authorize(
-        self, client: OAuthClientInformationFull, params: AuthorizationParams
-    ) -> str:
-        """Create an authorization URL for the OAuth flow.
-
-        For basic-memory, we'll implement a simple authorization flow.
-        In production, this might redirect to an external provider.
-        """
-        # Generate authorization code
-        auth_code = secrets.token_urlsafe(32)
-
-        # Store authorization code with metadata
-        self.authorization_codes[auth_code] = BasicMemoryAuthorizationCode(
-            code=auth_code,
-            scopes=params.scopes or [],
-            expires_at=(datetime.utcnow() + timedelta(minutes=10)).timestamp(),
-            client_id=client.client_id,
-            code_challenge=params.code_challenge,
-            redirect_uri=params.redirect_uri,
-            redirect_uri_provided_explicitly=params.redirect_uri_provided_explicitly,
-            issuer_state=params.state,
-        )
-
-        # In a real implementation, we'd redirect to an authorization page
-        # For now, we'll just return the redirect URL with the code
-        redirect_uri = str(params.redirect_uri)
-        separator = "&" if "?" in redirect_uri else "?"
-
-        auth_url = f"{redirect_uri}{separator}code={auth_code}"
-        if params.state:
-            auth_url += f"&state={params.state}"
-
-        return auth_url
-
-    async def load_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: str
-    ) -> Optional[BasicMemoryAuthorizationCode]:
-        """Load an authorization code."""
-        code = self.authorization_codes.get(authorization_code)
-
-        if code and code.client_id == client.client_id:
-            # Check if expired
-            if datetime.utcnow().timestamp() > code.expires_at:
-                del self.authorization_codes[authorization_code]
-                return None
-            return code
-
-        return None
-
-    async def exchange_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: BasicMemoryAuthorizationCode
-    ) -> OAuthToken:
-        """Exchange an authorization code for tokens."""
-        # Generate tokens
-        access_token = self._generate_access_token(client.client_id, authorization_code.scopes)
-        refresh_token = secrets.token_urlsafe(32)
-
-        # Store tokens
-        expires_at = (datetime.utcnow() + timedelta(hours=1)).timestamp()
-
-        self.access_tokens[access_token] = BasicMemoryAccessToken(
-            token=access_token,
-            client_id=client.client_id,
-            scopes=authorization_code.scopes,
-            expires_at=int(expires_at),
-        )
-
-        self.refresh_tokens[refresh_token] = BasicMemoryRefreshToken(
-            token=refresh_token,
-            client_id=client.client_id,
-            scopes=authorization_code.scopes,
-        )
-
-        # Remove used authorization code
-        del self.authorization_codes[authorization_code.code]
-
-        return OAuthToken(
-            access_token=access_token,
-            token_type="bearer",
-            expires_in=3600,  # 1 hour
-            refresh_token=refresh_token,
-            scope=" ".join(authorization_code.scopes) if authorization_code.scopes else None,
-        )
-
-    async def load_refresh_token(
-        self, client: OAuthClientInformationFull, refresh_token: str
-    ) -> Optional[BasicMemoryRefreshToken]:
-        """Load a refresh token."""
-        token = self.refresh_tokens.get(refresh_token)
-
-        if token and token.client_id == client.client_id:
-            return token
-
-        return None
-
-    async def exchange_refresh_token(
-        self,
-        client: OAuthClientInformationFull,
-        refresh_token: BasicMemoryRefreshToken,
-        scopes: list[str],
-    ) -> OAuthToken:
-        """Exchange a refresh token for new tokens."""
-        # Use requested scopes or original scopes
-        token_scopes = scopes if scopes else refresh_token.scopes
-
-        # Generate new tokens
-        new_access_token = self._generate_access_token(client.client_id, token_scopes)
-        new_refresh_token = secrets.token_urlsafe(32)
-
-        # Store new tokens
-        expires_at = (datetime.utcnow() + timedelta(hours=1)).timestamp()
-
-        self.access_tokens[new_access_token] = BasicMemoryAccessToken(
-            token=new_access_token,
-            client_id=client.client_id,
-            scopes=token_scopes,
-            expires_at=int(expires_at),
-        )
-
-        self.refresh_tokens[new_refresh_token] = BasicMemoryRefreshToken(
-            token=new_refresh_token,
-            client_id=client.client_id,
-            scopes=token_scopes,
-        )
-
-        # Remove old tokens
-        del self.refresh_tokens[refresh_token.token]
-
-        return OAuthToken(
-            access_token=new_access_token,
-            token_type="bearer",
-            expires_in=3600,  # 1 hour
-            refresh_token=new_refresh_token,
-            scope=" ".join(token_scopes) if token_scopes else None,
-        )
-
-    async def load_access_token(self, token: str) -> Optional[BasicMemoryAccessToken]:
-        """Load and validate an access token."""
-        logger.debug("Loading access token, checking in-memory store first")
-        access_token = self.access_tokens.get(token)
-
-        if access_token:
-            # Check if expired
-            if access_token.expires_at and datetime.utcnow().timestamp() > access_token.expires_at:
-                logger.debug("Token found in memory but expired, removing")
-                del self.access_tokens[token]
-                return None
-            logger.debug("Token found in memory and valid")
-            return access_token
-
-        # Try to decode as JWT
-        logger.debug("Token not in memory, attempting JWT decode with secret key")
-        try:
-            # Decode with audience verification - PyJWT expects the audience to match
-            payload = jwt.decode(
-                token,
-                self.secret_key,
-                algorithms=["HS256"],
-                audience="basic-memory",  # Expecting this audience
-                issuer=self.issuer_url,  # And this issuer
-            )
-            logger.debug(f"JWT decoded successfully: {payload}")
-            return BasicMemoryAccessToken(
-                token=token,
-                client_id=payload.get("sub", ""),
-                scopes=payload.get("scopes", []),
-                expires_at=payload.get("exp"),
-            )
-        except jwt.InvalidTokenError as e:
-            logger.error(f"JWT decode failed: {e}")
-            return None
-
-    async def revoke_token(self, token: BasicMemoryAccessToken | BasicMemoryRefreshToken) -> None:
-        """Revoke an access or refresh token."""
-        if isinstance(token, BasicMemoryAccessToken):
-            self.access_tokens.pop(token.token, None)
-        else:
-            self.refresh_tokens.pop(token.token, None)
-
-    def _generate_access_token(self, client_id: str, scopes: list[str]) -> str:
-        """Generate a JWT access token."""
-        payload = {
-            "iss": self.issuer_url,
-            "sub": client_id,
-            "aud": "basic-memory",
-            "exp": datetime.utcnow() + timedelta(hours=1),
-            "iat": datetime.utcnow(),
-            "scopes": scopes,
-        }
-
-        return jwt.encode(payload, self.secret_key, algorithm="HS256")

src/basic_memory/mcp/external_auth_provider.py

@@ -1,321 +0,0 @@
-"""External OAuth provider integration for Basic Memory MCP server."""
-
-import os
-from typing import Optional, Dict, Any
-from dataclasses import dataclass
-
-import httpx
-from loguru import logger
-from mcp.server.auth.provider import (
-    OAuthAuthorizationServerProvider,
-    AuthorizationParams,
-    AuthorizationCode,
-    RefreshToken,
-    AccessToken,
-    construct_redirect_uri,
-)
-from mcp.shared.auth import OAuthClientInformationFull, OAuthToken
-
-
-@dataclass
-class ExternalAuthorizationCode(AuthorizationCode):
-    """Authorization code with external provider metadata."""
-
-    external_code: Optional[str] = None
-    state: Optional[str] = None
-
-
-@dataclass
-class ExternalRefreshToken(RefreshToken):
-    """Refresh token with external provider metadata."""
-
-    external_token: Optional[str] = None
-
-
-@dataclass
-class ExternalAccessToken(AccessToken):
-    """Access token with external provider metadata."""
-
-    external_token: Optional[str] = None
-
-
-class ExternalOAuthProvider(
-    OAuthAuthorizationServerProvider[
-        ExternalAuthorizationCode, ExternalRefreshToken, ExternalAccessToken
-    ]
-):
-    """OAuth provider that delegates to external OAuth providers.
-
-    This provider can integrate with services like:
-    - GitHub OAuth
-    - Google OAuth
-    - Auth0
-    - Okta
-    """
-
-    def __init__(
-        self,
-        issuer_url: str,
-        external_provider: str,
-        external_client_id: str,
-        external_client_secret: str,
-        external_authorize_url: str,
-        external_token_url: str,
-        external_userinfo_url: Optional[str] = None,
-    ):
-        self.issuer_url = issuer_url
-        self.external_provider = external_provider
-        self.external_client_id = external_client_id
-        self.external_client_secret = external_client_secret
-        self.external_authorize_url = external_authorize_url
-        self.external_token_url = external_token_url
-        self.external_userinfo_url = external_userinfo_url
-
-        # In-memory storage - in production, use a database
-        self.clients: Dict[str, OAuthClientInformationFull] = {}
-        self.codes: Dict[str, ExternalAuthorizationCode] = {}
-        self.tokens: Dict[str, Any] = {}
-
-        self.http_client = httpx.AsyncClient()
-
-    async def get_client(self, client_id: str) -> Optional[OAuthClientInformationFull]:
-        """Get a client by ID."""
-        return self.clients.get(client_id)
-
-    async def register_client(self, client_info: OAuthClientInformationFull) -> None:
-        """Register a new OAuth client."""
-        self.clients[client_info.client_id] = client_info
-        logger.info(f"Registered external OAuth client: {client_info.client_id}")
-
-    async def authorize(
-        self, client: OAuthClientInformationFull, params: AuthorizationParams
-    ) -> str:
-        """Create authorization URL redirecting to external provider."""
-        # Store authorization request
-        import secrets
-
-        state = secrets.token_urlsafe(32)
-
-        self.codes[state] = ExternalAuthorizationCode(
-            code=state,
-            scopes=params.scopes or [],
-            expires_at=0,  # Will be set by external provider
-            client_id=client.client_id,
-            code_challenge=params.code_challenge,
-            redirect_uri=params.redirect_uri,
-            redirect_uri_provided_explicitly=params.redirect_uri_provided_explicitly,
-            state=params.state,
-        )
-
-        # Build external provider URL
-        external_params = {
-            "client_id": self.external_client_id,
-            "redirect_uri": f"{self.issuer_url}/callback",
-            "response_type": "code",
-            "state": state,
-            "scope": " ".join(params.scopes or []),
-        }
-
-        return construct_redirect_uri(self.external_authorize_url, **external_params)
-
-    async def handle_callback(self, code: str, state: str) -> str:
-        """Handle callback from external provider."""
-        # Get original authorization request
-        auth_code = self.codes.get(state)
-        if not auth_code:
-            raise ValueError("Invalid state parameter")
-
-        # Exchange code with external provider
-        token_data = {
-            "grant_type": "authorization_code",
-            "code": code,
-            "redirect_uri": f"{self.issuer_url}/callback",
-            "client_id": self.external_client_id,
-            "client_secret": self.external_client_secret,
-        }
-
-        response = await self.http_client.post(
-            self.external_token_url,
-            data=token_data,
-        )
-        response.raise_for_status()
-        external_tokens = response.json()
-
-        # Store external tokens
-        import secrets
-
-        internal_code = secrets.token_urlsafe(32)
-
-        self.codes[internal_code] = ExternalAuthorizationCode(
-            code=internal_code,
-            scopes=auth_code.scopes,
-            expires_at=0,
-            client_id=auth_code.client_id,
-            code_challenge=auth_code.code_challenge,
-            redirect_uri=auth_code.redirect_uri,
-            redirect_uri_provided_explicitly=auth_code.redirect_uri_provided_explicitly,
-            external_code=code,
-            state=auth_code.state,
-        )
-
-        self.tokens[internal_code] = external_tokens
-
-        # Redirect to original client
-        return construct_redirect_uri(
-            str(auth_code.redirect_uri),
-            code=internal_code,
-            state=auth_code.state,
-        )
-
-    async def load_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: str
-    ) -> Optional[ExternalAuthorizationCode]:
-        """Load an authorization code."""
-        code = self.codes.get(authorization_code)
-        if code and code.client_id == client.client_id:
-            return code
-        return None
-
-    async def exchange_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: ExternalAuthorizationCode
-    ) -> OAuthToken:
-        """Exchange authorization code for tokens."""
-        # Get stored external tokens
-        external_tokens = self.tokens.get(authorization_code.code)
-        if not external_tokens:
-            raise ValueError("No tokens found for authorization code")
-
-        # Map external tokens to MCP tokens
-        access_token = external_tokens.get("access_token")
-        refresh_token = external_tokens.get("refresh_token")
-        expires_in = external_tokens.get("expires_in", 3600)
-
-        # Store the mapping
-        self.tokens[access_token] = {
-            "client_id": client.client_id,
-            "external_token": access_token,
-            "scopes": authorization_code.scopes,
-        }
-
-        if refresh_token:
-            self.tokens[refresh_token] = {
-                "client_id": client.client_id,
-                "external_token": refresh_token,
-                "scopes": authorization_code.scopes,
-            }
-
-        # Clean up authorization code
-        del self.codes[authorization_code.code]
-
-        return OAuthToken(
-            access_token=access_token,
-            token_type="bearer",
-            expires_in=expires_in,
-            refresh_token=refresh_token,
-            scope=" ".join(authorization_code.scopes) if authorization_code.scopes else None,
-        )
-
-    async def load_refresh_token(
-        self, client: OAuthClientInformationFull, refresh_token: str
-    ) -> Optional[ExternalRefreshToken]:
-        """Load a refresh token."""
-        token_info = self.tokens.get(refresh_token)
-        if token_info and token_info["client_id"] == client.client_id:
-            return ExternalRefreshToken(
-                token=refresh_token,
-                client_id=client.client_id,
-                scopes=token_info["scopes"],
-                external_token=token_info.get("external_token"),
-            )
-        return None
-
-    async def exchange_refresh_token(
-        self,
-        client: OAuthClientInformationFull,
-        refresh_token: ExternalRefreshToken,
-        scopes: list[str],
-    ) -> OAuthToken:
-        """Exchange refresh token for new tokens."""
-        # Exchange with external provider
-        token_data = {
-            "grant_type": "refresh_token",
-            "refresh_token": refresh_token.external_token or refresh_token.token,
-            "client_id": self.external_client_id,
-            "client_secret": self.external_client_secret,
-        }
-
-        response = await self.http_client.post(
-            self.external_token_url,
-            data=token_data,
-        )
-        response.raise_for_status()
-        external_tokens = response.json()
-
-        # Update stored tokens
-        new_access_token = external_tokens.get("access_token")
-        new_refresh_token = external_tokens.get("refresh_token", refresh_token.token)
-        expires_in = external_tokens.get("expires_in", 3600)
-
-        self.tokens[new_access_token] = {
-            "client_id": client.client_id,
-            "external_token": new_access_token,
-            "scopes": scopes or refresh_token.scopes,
-        }
-
-        if new_refresh_token != refresh_token.token:
-            self.tokens[new_refresh_token] = {
-                "client_id": client.client_id,
-                "external_token": new_refresh_token,
-                "scopes": scopes or refresh_token.scopes,
-            }
-            del self.tokens[refresh_token.token]
-
-        return OAuthToken(
-            access_token=new_access_token,
-            token_type="bearer",
-            expires_in=expires_in,
-            refresh_token=new_refresh_token,
-            scope=" ".join(scopes or refresh_token.scopes),
-        )
-
-    async def load_access_token(self, token: str) -> Optional[ExternalAccessToken]:
-        """Load and validate an access token."""
-        token_info = self.tokens.get(token)
-        if token_info:
-            return ExternalAccessToken(
-                token=token,
-                client_id=token_info["client_id"],
-                scopes=token_info["scopes"],
-                external_token=token_info.get("external_token"),
-            )
-        return None
-
-    async def revoke_token(self, token: ExternalAccessToken | ExternalRefreshToken) -> None:
-        """Revoke a token."""
-        self.tokens.pop(token.token, None)
-
-
-def create_github_provider() -> ExternalOAuthProvider:
-    """Create an OAuth provider for GitHub integration."""
-    return ExternalOAuthProvider(
-        issuer_url=os.getenv("FASTMCP_AUTH_ISSUER_URL", "http://localhost:8000"),
-        external_provider="github",
-        external_client_id=os.getenv("GITHUB_CLIENT_ID", ""),
-        external_client_secret=os.getenv("GITHUB_CLIENT_SECRET", ""),
-        external_authorize_url="https://github.com/login/oauth/authorize",
-        external_token_url="https://github.com/login/oauth/access_token",
-        external_userinfo_url="https://api.github.com/user",
-    )
-
-
-def create_google_provider() -> ExternalOAuthProvider:
-    """Create an OAuth provider for Google integration."""
-    return ExternalOAuthProvider(
-        issuer_url=os.getenv("FASTMCP_AUTH_ISSUER_URL", "http://localhost:8000"),
-        external_provider="google",
-        external_client_id=os.getenv("GOOGLE_CLIENT_ID", ""),
-        external_client_secret=os.getenv("GOOGLE_CLIENT_SECRET", ""),
-        external_authorize_url="https://accounts.google.com/o/oauth2/v2/auth",
-        external_token_url="https://oauth2.googleapis.com/token",
-        external_userinfo_url="https://www.googleapis.com/oauth2/v1/userinfo",
-    )

src/basic_memory/mcp/project_session.py

@@ -8,7 +8,7 @@ from dataclasses import dataclass
 from typing import Optional
 from loguru import logger
 
-from basic_memory.config import ProjectConfig, get_project_config, config_manager
+from basic_memory.config import ProjectConfig, get_project_config, ConfigManager
 
 
 @dataclass
@@ -23,7 +23,7 @@ class ProjectSession:
     current_project: Optional[str] = None
     default_project: Optional[str] = None
 
-    def initialize(self, default_project: str) -> None:
+    def initialize(self, default_project: str) -> "ProjectSession":
         """Set the default project from config on startup.
 
         Args:
@@ -32,6 +32,7 @@ class ProjectSession:
         self.default_project = default_project
         self.current_project = default_project
         logger.info(f"Initialized project session with default project: {default_project}")
+        return self
 
     def get_current_project(self) -> str:
         """Get the currently active project name.
@@ -72,7 +73,7 @@ class ProjectSession:
         via CLI or API to ensure MCP session stays in sync.
         """
         # Reload config to get latest default project
-        current_config = config_manager.load_config()
+        current_config = ConfigManager().config
         new_default = current_config.default_project
 
         # Reinitialize with new default
@@ -102,7 +103,8 @@ def get_active_project(project_override: Optional[str] = None) -> ProjectConfig:
         return project
 
     current_project = session.get_current_project()
-    return get_project_config(current_project)
+    active_project = get_project_config(current_project)
+    return active_project
 
 
 def add_project_metadata(result: str, project_name: str) -> str:

src/basic_memory/mcp/prompts/__init__.py

@@ -10,12 +10,10 @@ from basic_memory.mcp.prompts import continue_conversation
 from basic_memory.mcp.prompts import recent_activity
 from basic_memory.mcp.prompts import search
 from basic_memory.mcp.prompts import ai_assistant_guide
-from basic_memory.mcp.prompts import sync_status
 
 __all__ = [
     "ai_assistant_guide",
     "continue_conversation",
     "recent_activity",
     "search",
-    "sync_status",
 ]

src/basic_memory/mcp/prompts/sync_status.py

@@ -1,112 +0,0 @@
-"""Sync status prompt for Basic Memory MCP server."""
-
-from basic_memory.mcp.server import mcp
-
-
-@mcp.prompt(
-    description="""Get sync status with recommendations for AI assistants.
-    
-    This prompt provides both current sync status and guidance on how
-    AI assistants should respond when sync operations are in progress or completed.
-    """,
-)
-async def sync_status_prompt() -> str:
-    """Get sync status with AI assistant guidance.
-    Returns:
-        Formatted sync status with AI assistant guidance
-    """
-    try:  # pragma: no cover
-        from basic_memory.services.migration_service import migration_manager
-
-        state = migration_manager.state
-
-        # Build status report
-        lines = [
-            "# Basic Memory Sync Status",
-            "",
-            f"**Current Status**: {state.status.value.replace('_', ' ').title()}",
-            f"**System Ready**: {'Yes' if migration_manager.is_ready else 'No'}",
-            "",
-        ]
-
-        if migration_manager.is_ready:
-            lines.extend(
-                [
-                    "✅ **All sync operations completed** - System is fully operational",
-                    "",
-                    "All Basic Memory tools are available and functioning normally.",
-                    "File indexing is complete and knowledge graphs are up to date.",
-                    "You can proceed with any knowledge management tasks.",
-                ]
-            )
-        else:
-            lines.append(f"**Status Message**: {state.message}")
-
-            if state.status.value == "in_progress":
-                if state.projects_total > 0:
-                    progress = f" ({state.projects_migrated}/{state.projects_total})"
-                    lines.append(f"**Progress**: {progress}")
-
-                lines.extend(
-                    [
-                        "",
-                        "🔄 **File synchronization in progress** - Processing files and building knowledge graphs",
-                        "",
-                        "**Impact**: Some tools may show status messages instead of normal responses",
-                        "until sync completes (usually 1-3 minutes).",
-                    ]
-                )
-
-            elif state.status.value == "failed":
-                lines.extend(
-                    [
-                        "",
-                        f"❌ **Sync failed**: {state.error or 'Unknown error'}",
-                        "",
-                        "**Impact**: System may have limited functionality until issue is resolved.",
-                    ]
-                )
-
-        # Add AI assistant recommendations
-        if not migration_manager.is_ready:
-            lines.extend(
-                [
-                    "",
-                    "---",
-                    "",
-                    "## AI Assistant Recommendations",
-                    "",
-                    "**When sync is in progress:**",
-                    "- Inform the user about the background file processing",
-                    "- Suggest using `sync_status()` tool to check progress",
-                    "- Explain that tools will work normally once sync completes",
-                    "- Avoid creating complex workflows until sync is done",
-                    "",
-                    "**What to tell users:**",
-                    "- 'Basic Memory is processing your files and building knowledge graphs'",
-                    "- 'This usually takes 1-3 minutes depending on your content size'",
-                    "- 'You can check progress anytime with the sync_status tool'",
-                    "- 'Full functionality will be available once processing completes'",
-                    "",
-                    "**User-friendly language:**",
-                    "- Say 'processing files' instead of 'migration' or 'sync'",
-                    "- Say 'building knowledge graphs' instead of 'indexing'",
-                    "- Say 'setting up your knowledge base' instead of 'running migrations'",
-                ]
-            )
-
-        return "\n".join(lines)
-
-    except Exception as e:  # pragma: no cover
-        return f"""# Sync Status - Error
-
-❌ **Unable to check sync status**: {str(e)}
-
-## AI Assistant Recommendations
-
-**When status is unavailable:**
-- Assume the system is likely working normally
-- Try proceeding with normal operations
-- If users report issues, suggest checking logs or restarting
-- Use user-friendly language about 'setting up the knowledge base'
-"""

src/basic_memory/mcp/server.py

@@ -7,25 +7,10 @@ from contextlib import asynccontextmanager
 from dataclasses import dataclass
 from typing import AsyncIterator, Optional, Any
 
-from dotenv import load_dotenv
 from fastmcp import FastMCP
-from fastmcp.utilities.logging import configure_logging as mcp_configure_logging
-from mcp.server.auth.settings import AuthSettings
 
-from basic_memory.config import app_config
+from basic_memory.config import ConfigManager
 from basic_memory.services.initialization import initialize_app
-from basic_memory.mcp.auth_provider import BasicMemoryOAuthProvider
-from basic_memory.mcp.project_session import session
-from basic_memory.mcp.external_auth_provider import (
-    create_github_provider,
-    create_google_provider,
-)
-from basic_memory.mcp.supabase_auth_provider import SupabaseOAuthProvider
-
-# mcp console logging
-mcp_configure_logging(level="ERROR")
-
-load_dotenv()
 
 
 @dataclass
@@ -36,7 +21,11 @@ class AppContext:
 
 @asynccontextmanager
 async def app_lifespan(server: FastMCP) -> AsyncIterator[AppContext]:  # pragma: no cover
-    """Manage application lifecycle with type-safe context"""
+    """ """
+    # defer import so tests can monkeypatch
+    from basic_memory.mcp.project_session import session
+
+    app_config = ConfigManager().config
     # Initialize on startup (now returns migration_manager)
     migration_manager = await initialize_app(app_config)
 
@@ -50,60 +39,8 @@ async def app_lifespan(server: FastMCP) -> AsyncIterator[AppContext]:  # pragma:
         pass
 
 
-# OAuth configuration function
-def create_auth_config() -> tuple[AuthSettings | None, Any | None]:
-    """Create OAuth configuration if enabled."""
-    # Check if OAuth is enabled via environment variable
-    import os
-
-    if os.getenv("FASTMCP_AUTH_ENABLED", "false").lower() == "true":
-        from pydantic import AnyHttpUrl
-
-        # Configure OAuth settings
-        issuer_url = os.getenv("FASTMCP_AUTH_ISSUER_URL", "http://localhost:8000")
-        required_scopes = os.getenv("FASTMCP_AUTH_REQUIRED_SCOPES", "read,write")
-        docs_url = os.getenv("FASTMCP_AUTH_DOCS_URL") or "http://localhost:8000/docs/oauth"
-
-        auth_settings = AuthSettings(
-            issuer_url=AnyHttpUrl(issuer_url),
-            service_documentation_url=AnyHttpUrl(docs_url),
-            required_scopes=required_scopes.split(",") if required_scopes else ["read", "write"],
-        )
-
-        # Create OAuth provider based on type
-        provider_type = os.getenv("FASTMCP_AUTH_PROVIDER", "basic").lower()
-
-        if provider_type == "github":
-            auth_provider = create_github_provider()
-        elif provider_type == "google":
-            auth_provider = create_google_provider()
-        elif provider_type == "supabase":
-            supabase_url = os.getenv("SUPABASE_URL")
-            supabase_anon_key = os.getenv("SUPABASE_ANON_KEY")
-            supabase_service_key = os.getenv("SUPABASE_SERVICE_KEY")
-
-            if not supabase_url or not supabase_anon_key:
-                raise ValueError("SUPABASE_URL and SUPABASE_ANON_KEY must be set for Supabase auth")
-
-            auth_provider = SupabaseOAuthProvider(
-                supabase_url=supabase_url,
-                supabase_anon_key=supabase_anon_key,
-                supabase_service_key=supabase_service_key,
-                issuer_url=issuer_url,
-            )
-        else:  # default to "basic"
-            auth_provider = BasicMemoryOAuthProvider(issuer_url=issuer_url)
-
-        return auth_settings, auth_provider
-
-    return None, None
-
-
-# Create auth configuration
-auth_settings, auth_provider = create_auth_config()
-
-# Create the shared server instance
+# Create the shared server instance with custom Stytch auth
 mcp = FastMCP(
     name="Basic Memory",
-    auth=auth_provider,
+    lifespan=app_lifespan,
 )

src/basic_memory/mcp/supabase_auth_provider.py

@@ -1,463 +0,0 @@
-"""Supabase OAuth provider for Basic Memory MCP server."""
-
-import os
-import secrets
-from dataclasses import dataclass
-from datetime import datetime, timedelta
-from typing import Optional, Dict, Any
-
-import httpx
-import jwt
-from loguru import logger
-from mcp.server.auth.provider import (
-    OAuthAuthorizationServerProvider,
-    AuthorizationParams,
-    AuthorizationCode,
-    RefreshToken,
-    AccessToken,
-    TokenError,
-    AuthorizeError,
-)
-from mcp.shared.auth import OAuthClientInformationFull, OAuthToken
-
-
-@dataclass
-class SupabaseAuthorizationCode(AuthorizationCode):
-    """Authorization code with Supabase metadata."""
-
-    user_id: Optional[str] = None
-    email: Optional[str] = None
-
-
-@dataclass
-class SupabaseRefreshToken(RefreshToken):
-    """Refresh token with Supabase metadata."""
-
-    supabase_refresh_token: Optional[str] = None
-    user_id: Optional[str] = None
-
-
-@dataclass
-class SupabaseAccessToken(AccessToken):
-    """Access token with Supabase metadata."""
-
-    supabase_access_token: Optional[str] = None
-    user_id: Optional[str] = None
-    email: Optional[str] = None
-
-
-class SupabaseOAuthProvider(
-    OAuthAuthorizationServerProvider[
-        SupabaseAuthorizationCode, SupabaseRefreshToken, SupabaseAccessToken
-    ]
-):
-    """OAuth provider that integrates with Supabase Auth.
-
-    This provider uses Supabase as the authentication backend while
-    maintaining compatibility with MCP's OAuth requirements.
-    """
-
-    def __init__(
-        self,
-        supabase_url: str,
-        supabase_anon_key: str,
-        supabase_service_key: Optional[str] = None,
-        issuer_url: str = "http://localhost:8000",
-    ):
-        self.supabase_url = supabase_url.rstrip("/")
-        self.supabase_anon_key = supabase_anon_key
-        self.supabase_service_key = supabase_service_key or supabase_anon_key
-        self.issuer_url = issuer_url
-
-        # HTTP client for Supabase API calls
-        self.http_client = httpx.AsyncClient()
-
-        # Temporary storage for auth flows (in production, use Supabase DB)
-        self.pending_auth_codes: Dict[str, SupabaseAuthorizationCode] = {}
-        self.mcp_to_supabase_tokens: Dict[str, Dict[str, Any]] = {}
-
-    async def get_client(self, client_id: str) -> Optional[OAuthClientInformationFull]:
-        """Get a client from Supabase.
-
-        In production, this would query a clients table in Supabase.
-        """
-        # For now, we'll validate against a configured list of allowed clients
-        # In production, query Supabase DB for client info
-        allowed_clients = os.getenv("SUPABASE_ALLOWED_CLIENTS", "").split(",")
-
-        if client_id in allowed_clients:
-            return OAuthClientInformationFull(
-                client_id=client_id,
-                client_secret="",  # Supabase handles secrets
-                redirect_uris=[],  # Supabase handles redirect URIs
-            )
-
-        return None
-
-    async def register_client(self, client_info: OAuthClientInformationFull) -> None:
-        """Register a new OAuth client in Supabase.
-
-        In production, this would insert into a clients table.
-        """
-        # For development, we just log the registration
-        logger.info(f"Would register client {client_info.client_id} in Supabase")
-
-        # In production:
-        # await self.supabase.table('oauth_clients').insert({
-        #     'client_id': client_info.client_id,
-        #     'client_secret': client_info.client_secret,
-        #     'metadata': client_info.client_metadata,
-        # }).execute()
-
-    async def authorize(
-        self, client: OAuthClientInformationFull, params: AuthorizationParams
-    ) -> str:
-        """Create authorization URL redirecting to Supabase Auth.
-
-        This initiates the OAuth flow with Supabase as the identity provider.
-        """
-        # Generate state for this auth request
-        state = secrets.token_urlsafe(32)
-
-        # Store the authorization request
-        self.pending_auth_codes[state] = SupabaseAuthorizationCode(
-            code=state,
-            scopes=params.scopes or [],
-            expires_at=(datetime.utcnow() + timedelta(minutes=10)).timestamp(),
-            client_id=client.client_id,
-            code_challenge=params.code_challenge,
-            redirect_uri=params.redirect_uri,
-            redirect_uri_provided_explicitly=params.redirect_uri_provided_explicitly,
-        )
-
-        # Build Supabase auth URL
-        auth_params = {
-            "redirect_to": f"{self.issuer_url}/auth/callback",
-            "scopes": " ".join(params.scopes or ["openid", "email"]),
-            "state": state,
-        }
-
-        # Use Supabase's OAuth endpoint
-        auth_url = f"{self.supabase_url}/auth/v1/authorize"
-        query_string = "&".join(f"{k}={v}" for k, v in auth_params.items())
-
-        return f"{auth_url}?{query_string}"
-
-    async def handle_supabase_callback(self, code: str, state: str) -> str:
-        """Handle callback from Supabase after user authentication."""
-        # Get the original auth request
-        auth_request = self.pending_auth_codes.get(state)
-        if not auth_request:
-            raise AuthorizeError(
-                error="invalid_request",
-                error_description="Invalid state parameter",
-            )
-
-        # Exchange code with Supabase for tokens
-        token_response = await self.http_client.post(
-            f"{self.supabase_url}/auth/v1/token",
-            json={
-                "grant_type": "authorization_code",
-                "code": code,
-                "redirect_uri": f"{self.issuer_url}/auth/callback",
-            },
-            headers={
-                "apikey": self.supabase_anon_key,
-                "Authorization": f"Bearer {self.supabase_anon_key}",
-            },
-        )
-
-        if not token_response.is_success:
-            raise AuthorizeError(
-                error="server_error",
-                error_description="Failed to exchange code with Supabase",
-            )
-
-        supabase_tokens = token_response.json()
-
-        # Get user info from Supabase
-        user_response = await self.http_client.get(
-            f"{self.supabase_url}/auth/v1/user",
-            headers={
-                "apikey": self.supabase_anon_key,
-                "Authorization": f"Bearer {supabase_tokens['access_token']}",
-            },
-        )
-
-        user_data = user_response.json() if user_response.is_success else {}
-
-        # Generate MCP authorization code
-        mcp_code = secrets.token_urlsafe(32)
-
-        # Update auth request with user info
-        auth_request.code = mcp_code
-        auth_request.user_id = user_data.get("id")
-        auth_request.email = user_data.get("email")
-
-        # Store mapping
-        self.pending_auth_codes[mcp_code] = auth_request
-        self.mcp_to_supabase_tokens[mcp_code] = {
-            "supabase_tokens": supabase_tokens,
-            "user": user_data,
-        }
-
-        # Clean up old state
-        del self.pending_auth_codes[state]
-
-        # Redirect back to client
-        redirect_uri = str(auth_request.redirect_uri)
-        separator = "&" if "?" in redirect_uri else "?"
-
-        return f"{redirect_uri}{separator}code={mcp_code}&state={state}"
-
-    async def load_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: str
-    ) -> Optional[SupabaseAuthorizationCode]:
-        """Load an authorization code."""
-        code = self.pending_auth_codes.get(authorization_code)
-
-        if code and code.client_id == client.client_id:
-            # Check expiration
-            if datetime.utcnow().timestamp() > code.expires_at:
-                del self.pending_auth_codes[authorization_code]
-                return None
-            return code
-
-        return None
-
-    async def exchange_authorization_code(
-        self, client: OAuthClientInformationFull, authorization_code: SupabaseAuthorizationCode
-    ) -> OAuthToken:
-        """Exchange authorization code for tokens."""
-        # Get stored Supabase tokens
-        token_data = self.mcp_to_supabase_tokens.get(authorization_code.code)
-        if not token_data:
-            raise TokenError(error="invalid_grant", error_description="Invalid authorization code")
-
-        supabase_tokens = token_data["supabase_tokens"]
-        user = token_data["user"]
-
-        # Generate MCP tokens that wrap Supabase tokens
-        access_token = self._generate_mcp_token(
-            client_id=client.client_id,
-            user_id=user.get("id", ""),
-            email=user.get("email", ""),
-            scopes=authorization_code.scopes,
-            supabase_access_token=supabase_tokens["access_token"],
-        )
-
-        refresh_token = secrets.token_urlsafe(32)
-
-        # Store the token mapping
-        self.mcp_to_supabase_tokens[access_token] = {
-            "client_id": client.client_id,
-            "user_id": user.get("id"),
-            "email": user.get("email"),
-            "supabase_access_token": supabase_tokens["access_token"],
-            "supabase_refresh_token": supabase_tokens["refresh_token"],
-            "scopes": authorization_code.scopes,
-        }
-
-        # Store refresh token mapping
-        self.mcp_to_supabase_tokens[refresh_token] = {
-            "client_id": client.client_id,
-            "user_id": user.get("id"),
-            "supabase_refresh_token": supabase_tokens["refresh_token"],
-            "scopes": authorization_code.scopes,
-        }
-
-        # Clean up authorization code
-        del self.pending_auth_codes[authorization_code.code]
-        del self.mcp_to_supabase_tokens[authorization_code.code]
-
-        return OAuthToken(
-            access_token=access_token,
-            token_type="bearer",
-            expires_in=supabase_tokens.get("expires_in", 3600),
-            refresh_token=refresh_token,
-            scope=" ".join(authorization_code.scopes) if authorization_code.scopes else None,
-        )
-
-    async def load_refresh_token(
-        self, client: OAuthClientInformationFull, refresh_token: str
-    ) -> Optional[SupabaseRefreshToken]:
-        """Load a refresh token."""
-        token_data = self.mcp_to_supabase_tokens.get(refresh_token)
-
-        if token_data and token_data["client_id"] == client.client_id:
-            return SupabaseRefreshToken(
-                token=refresh_token,
-                client_id=client.client_id,
-                scopes=token_data["scopes"],
-                supabase_refresh_token=token_data["supabase_refresh_token"],
-                user_id=token_data.get("user_id"),
-            )
-
-        return None
-
-    async def exchange_refresh_token(
-        self,
-        client: OAuthClientInformationFull,
-        refresh_token: SupabaseRefreshToken,
-        scopes: list[str],
-    ) -> OAuthToken:
-        """Exchange refresh token for new tokens using Supabase."""
-        # Refresh with Supabase
-        token_response = await self.http_client.post(
-            f"{self.supabase_url}/auth/v1/token",
-            json={
-                "grant_type": "refresh_token",
-                "refresh_token": refresh_token.supabase_refresh_token,
-            },
-            headers={
-                "apikey": self.supabase_anon_key,
-                "Authorization": f"Bearer {self.supabase_anon_key}",
-            },
-        )
-
-        if not token_response.is_success:
-            raise TokenError(
-                error="invalid_grant",
-                error_description="Failed to refresh with Supabase",
-            )
-
-        supabase_tokens = token_response.json()
-
-        # Get updated user info
-        user_response = await self.http_client.get(
-            f"{self.supabase_url}/auth/v1/user",
-            headers={
-                "apikey": self.supabase_anon_key,
-                "Authorization": f"Bearer {supabase_tokens['access_token']}",
-            },
-        )
-
-        user_data = user_response.json() if user_response.is_success else {}
-
-        # Generate new MCP tokens
-        new_access_token = self._generate_mcp_token(
-            client_id=client.client_id,
-            user_id=user_data.get("id", ""),
-            email=user_data.get("email", ""),
-            scopes=scopes or refresh_token.scopes,
-            supabase_access_token=supabase_tokens["access_token"],
-        )
-
-        new_refresh_token = secrets.token_urlsafe(32)
-
-        # Update token mappings
-        self.mcp_to_supabase_tokens[new_access_token] = {
-            "client_id": client.client_id,
-            "user_id": user_data.get("id"),
-            "email": user_data.get("email"),
-            "supabase_access_token": supabase_tokens["access_token"],
-            "supabase_refresh_token": supabase_tokens["refresh_token"],
-            "scopes": scopes or refresh_token.scopes,
-        }
-
-        self.mcp_to_supabase_tokens[new_refresh_token] = {
-            "client_id": client.client_id,
-            "user_id": user_data.get("id"),
-            "supabase_refresh_token": supabase_tokens["refresh_token"],
-            "scopes": scopes or refresh_token.scopes,
-        }
-
-        # Clean up old tokens
-        del self.mcp_to_supabase_tokens[refresh_token.token]
-
-        return OAuthToken(
-            access_token=new_access_token,
-            token_type="bearer",
-            expires_in=supabase_tokens.get("expires_in", 3600),
-            refresh_token=new_refresh_token,
-            scope=" ".join(scopes or refresh_token.scopes),
-        )
-
-    async def load_access_token(self, token: str) -> Optional[SupabaseAccessToken]:
-        """Load and validate an access token."""
-        # First check our mapping
-        token_data = self.mcp_to_supabase_tokens.get(token)
-        if token_data:
-            return SupabaseAccessToken(
-                token=token,
-                client_id=token_data["client_id"],
-                scopes=token_data["scopes"],
-                supabase_access_token=token_data.get("supabase_access_token"),
-                user_id=token_data.get("user_id"),
-                email=token_data.get("email"),
-            )
-
-        # Try to decode as JWT
-        try:
-            # Verify with Supabase's JWT secret
-            payload = jwt.decode(
-                token,
-                os.getenv("SUPABASE_JWT_SECRET", ""),
-                algorithms=["HS256"],
-                audience="authenticated",
-            )
-
-            return SupabaseAccessToken(
-                token=token,
-                client_id=payload.get("client_id", ""),
-                scopes=payload.get("scopes", []),
-                user_id=payload.get("sub"),
-                email=payload.get("email"),
-            )
-        except jwt.InvalidTokenError:
-            pass
-
-        # Validate with Supabase
-        user_response = await self.http_client.get(
-            f"{self.supabase_url}/auth/v1/user",
-            headers={
-                "apikey": self.supabase_anon_key,
-                "Authorization": f"Bearer {token}",
-            },
-        )
-
-        if user_response.is_success:
-            user_data = user_response.json()
-            return SupabaseAccessToken(
-                token=token,
-                client_id="",  # Unknown client for direct Supabase tokens
-                scopes=[],
-                supabase_access_token=token,
-                user_id=user_data.get("id"),
-                email=user_data.get("email"),
-            )
-
-        return None
-
-    async def revoke_token(self, token: SupabaseAccessToken | SupabaseRefreshToken) -> None:
-        """Revoke a token."""
-        # Remove from our mapping
-        self.mcp_to_supabase_tokens.pop(token.token, None)
-
-        # In production, also revoke in Supabase:
-        # await self.supabase.auth.admin.sign_out(token.user_id)
-
-    def _generate_mcp_token(
-        self,
-        client_id: str,
-        user_id: str,
-        email: str,
-        scopes: list[str],
-        supabase_access_token: str,
-    ) -> str:
-        """Generate an MCP token that wraps Supabase authentication."""
-        payload = {
-            "iss": self.issuer_url,
-            "sub": user_id,
-            "client_id": client_id,
-            "email": email,
-            "scopes": scopes,
-            "supabase_token": supabase_access_token[:10] + "...",  # Reference only
-            "exp": datetime.utcnow() + timedelta(hours=1),
-            "iat": datetime.utcnow(),
-        }
-
-        # Use Supabase JWT secret if available
-        secret = os.getenv("SUPABASE_JWT_SECRET", secrets.token_urlsafe(32))
-
-        return jwt.encode(payload, secret, algorithm="HS256")

src/basic_memory/mcp/tools/__init__.py

@@ -20,24 +20,24 @@ from basic_memory.mcp.tools.edit_note import edit_note
 from basic_memory.mcp.tools.move_note import move_note
 from basic_memory.mcp.tools.sync_status import sync_status
 from basic_memory.mcp.tools.project_management import (
-    list_projects,
+    list_memory_projects,
     switch_project,
     get_current_project,
     set_default_project,
-    create_project,
+    create_memory_project,
     delete_project,
 )
 
 __all__ = [
     "build_context",
     "canvas",
-    "create_project",
+    "create_memory_project",
     "delete_note",
     "delete_project",
     "edit_note",
     "get_current_project",
     "list_directory",
-    "list_projects",
+    "list_memory_projects",
     "move_note",
     "read_content",
     "read_note",

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,
@@ -80,12 +81,26 @@ 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
+    active_project = get_active_project(project)
+
     # Check migration status and wait briefly if needed
     from basic_memory.mcp.tools.utils import wait_for_migration_or_return_status
 
-    migration_status = await wait_for_migration_or_return_status(timeout=5.0)
+    migration_status = await wait_for_migration_or_return_status(
+        timeout=5.0, project_name=active_project.name
+    )
     if migration_status:  # pragma: no cover
         # Return a proper GraphContext with status message
         from basic_memory.schemas.memory import MemoryMetadata
@@ -96,14 +111,12 @@ 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
             ),
         )
-
-    active_project = get_active_project(project)
     project_url = active_project.project_url
 
     response = await call_get(

src/basic_memory/mcp/tools/move_note.py

@@ -7,9 +7,145 @@ from loguru import logger
 
 from basic_memory.mcp.async_client import client
 from basic_memory.mcp.server import mcp
-from basic_memory.mcp.tools.utils import call_post
+from basic_memory.mcp.tools.utils import call_post, call_get
 from basic_memory.mcp.project_session import get_active_project
 from basic_memory.schemas import EntityResponse
+from basic_memory.schemas.project_info import ProjectList
+from basic_memory.utils import validate_project_path
+
+
+async def _detect_cross_project_move_attempt(
+    identifier: str, destination_path: str, current_project: str
+) -> Optional[str]:
+    """Detect potential cross-project move attempts and return guidance.
+
+    Args:
+        identifier: The note identifier being moved
+        destination_path: The destination path
+        current_project: The current active project
+
+    Returns:
+        Error message with guidance if cross-project move is detected, None otherwise
+    """
+    try:
+        # Get list of all available projects to check against
+        response = await call_get(client, "/projects/projects")
+        project_list = ProjectList.model_validate(response.json())
+        project_names = [p.name.lower() for p in project_list.projects]
+
+        # Check if destination path contains any project names
+        dest_lower = destination_path.lower()
+        path_parts = dest_lower.split("/")
+
+        # Look for project names in the destination path
+        for part in path_parts:
+            if part in project_names and part != current_project.lower():
+                # Found a different project name in the path
+                matching_project = next(
+                    p.name for p in project_list.projects if p.name.lower() == part
+                )
+                return _format_cross_project_error_response(
+                    identifier, destination_path, current_project, matching_project
+                )
+
+        # No other cross-project patterns detected
+
+    except Exception as e:
+        # If we can't detect, don't interfere with normal error handling
+        logger.debug(f"Could not check for cross-project move: {e}")
+        return None
+
+    return None
+
+
+def _format_cross_project_error_response(
+    identifier: str, destination_path: str, current_project: str, target_project: str
+) -> str:
+    """Format error response for detected cross-project move attempts."""
+    return dedent(f"""
+        # Move Failed - Cross-Project Move Not Supported
+        
+        Cannot move '{identifier}' to '{destination_path}' because it appears to reference a different project ('{target_project}').
+        
+        **Current project:** {current_project}
+        **Target project:** {target_project}
+        
+        ## Cross-project moves are not supported directly
+        
+        Notes can only be moved within the same project. To move content between projects, use this workflow:
+        
+        ### Recommended approach:
+        ```
+        # 1. Read the note content from current project
+        read_note("{identifier}")
+        
+        # 2. Switch to the target project
+        switch_project("{target_project}")
+        
+        # 3. Create the note in the target project
+        write_note("Note Title", "content from step 1", "target-folder")
+        
+        # 4. Switch back to original project (optional)
+        switch_project("{current_project}")
+        
+        # 5. Delete the original note if desired
+        delete_note("{identifier}")
+        ```
+        
+        ### Alternative: Stay in current project
+        If you want to move the note within the **{current_project}** project only:
+        ```
+        move_note("{identifier}", "new-folder/new-name.md")
+        ```
+        
+        ## Available projects:
+        Use `list_projects()` to see all available projects and `switch_project("project-name")` to change projects.
+        """).strip()
+
+
+def _format_potential_cross_project_guidance(
+    identifier: str, destination_path: str, current_project: str, available_projects: list[str]
+) -> str:
+    """Format guidance for potentially cross-project moves."""
+    other_projects = ", ".join(available_projects[:3])  # Show first 3 projects
+    if len(available_projects) > 3:
+        other_projects += f" (and {len(available_projects) - 3} others)"
+
+    return dedent(f"""
+        # Move Failed - Check Project Context
+        
+        Cannot move '{identifier}' to '{destination_path}' within the current project '{current_project}'.
+        
+        ## If you intended to move within the current project:
+        The destination path should be relative to the project root:
+        ```
+        move_note("{identifier}", "folder/filename.md")
+        ```
+        
+        ## If you intended to move to a different project:
+        Cross-project moves require switching projects first. Available projects: {other_projects}
+        
+        ### To move to another project:
+        ```
+        # 1. Read the content
+        read_note("{identifier}")
+        
+        # 2. Switch to target project
+        switch_project("target-project-name")
+        
+        # 3. Create note in target project
+        write_note("Title", "content", "folder")
+        
+        # 4. Switch back and delete original if desired
+        switch_project("{current_project}")
+        delete_note("{identifier}")
+        ```
+        
+        ### To see all projects:
+        ```
+        list_projects()
+        ```
+        """).strip()
 
 
 def _format_move_error_response(error_message: str, identifier: str, destination_path: str) -> str:
@@ -258,6 +394,36 @@ async def move_note(
     active_project = get_active_project(project)
     project_url = active_project.project_url
 
+    # Validate destination path to prevent path traversal attacks
+    project_path = active_project.home
+    if not validate_project_path(destination_path, project_path):
+        logger.warning(
+            "Attempted path traversal attack blocked",
+            destination_path=destination_path,
+            project=active_project.name,
+        )
+        return f"""# Move Failed - Security Validation Error
+
+The destination path '{destination_path}' is not allowed - paths must stay within project boundaries.
+
+## Valid path examples:
+- `notes/my-file.md`
+- `projects/2025/meeting-notes.md`
+- `archive/old-notes.md`
+
+## Try again with a safe path:
+```
+move_note("{identifier}", "notes/{destination_path.split("/")[-1] if "/" in destination_path else destination_path}")
+```"""
+
+    # Check for potential cross-project move attempts
+    cross_project_error = await _detect_cross_project_move_attempt(
+        identifier, destination_path, active_project.name
+    )
+    if cross_project_error:
+        logger.info(f"Detected cross-project move attempt: {identifier} -> {destination_path}")
+        return cross_project_error
+
     try:
         # Prepare move request
         move_data = {

src/basic_memory/mcp/tools/project_management.py

@@ -5,6 +5,7 @@ and manage project context during conversations.
 """
 
 from textwrap import dedent
+from typing import Optional
 
 from fastmcp import Context
 from loguru import logger
@@ -19,7 +20,9 @@ from basic_memory.utils import generate_permalink
 
 
 @mcp.tool("list_memory_projects")
-async def list_projects(ctx: Context | None = None) -> str:
+async def list_memory_projects(
+    ctx: Context | None = None, _compatibility: Optional[str] = None
+) -> str:
     """List all available projects with their status.
 
     Shows all Basic Memory projects that are available, indicating which one
@@ -29,7 +32,7 @@ async def list_projects(ctx: Context | None = None) -> str:
         Formatted list of projects with status indicators
 
     Example:
-        list_projects()
+        list_memory_projects()
     """
     if ctx:  # pragma: no cover
         await ctx.info("Listing all available projects")
@@ -144,13 +147,13 @@ async def switch_project(project_name: str, ctx: Context | None = None) -> str:
             Your session remains on the previous project.
 
             ## Troubleshooting:
-            1. **Check available projects**: Use `list_projects()` to see valid project names
+            1. **Check available projects**: Use `list_memory_projects()` to see valid project names
             2. **Verify spelling**: Ensure the project name is spelled correctly
             3. **Check permissions**: Verify you have access to the requested project
             4. **Try again**: The error might be temporary
 
             ## Available options:
-            - See all projects: `list_projects()`
+            - See all projects: `list_memory_projects()`
             - Stay on current project: `get_current_project()`
             - Try different project: `switch_project("correct-project-name")`
 
@@ -159,7 +162,9 @@ async def switch_project(project_name: str, ctx: Context | None = None) -> str:
 
 
 @mcp.tool()
-async def get_current_project(ctx: Context | None = None) -> str:
+async def get_current_project(
+    ctx: Context | None = None, _compatibility: Optional[str] = None
+) -> str:
     """Show the currently active project and basic stats.
 
     Displays which project is currently active and provides basic information
@@ -216,8 +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"
@@ -231,7 +238,7 @@ async def set_default_project(project_name: str, ctx: Context | None = None) ->
 
 
 @mcp.tool("create_memory_project")
-async def create_project(
+async def create_memory_project(
     project_name: str, project_path: str, set_default: bool = False, ctx: Context | None = None
 ) -> str:
     """Create a new Basic Memory project.
@@ -248,8 +255,8 @@ async def create_project(
         Confirmation message with project details
 
     Example:
-        create_project("my-research", "~/Documents/research")
-        create_project("work-notes", "/home/user/work", set_default=True)
+        create_memory_project("my-research", "~/Documents/research")
+        create_memory_project("work-notes", "/home/user/work", set_default=True)
     """
     if ctx:  # pragma: no cover
         await ctx.info(f"Creating project: {project_name} at {project_path}")
@@ -318,16 +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_content.py

@@ -17,6 +17,7 @@ from basic_memory.mcp.async_client import client
 from basic_memory.mcp.tools.utils import call_get
 from basic_memory.mcp.project_session import get_active_project
 from basic_memory.schemas.memory import memory_url_path
+from basic_memory.utils import validate_project_path
 
 
 def calculate_target_params(content_length):
@@ -188,6 +189,21 @@ async def read_content(path: str, project: Optional[str] = None) -> dict:
     project_url = active_project.project_url
 
     url = memory_url_path(path)
+
+    # Validate path to prevent path traversal attacks
+    project_path = active_project.home
+    if not validate_project_path(url, project_path):
+        logger.warning(
+            "Attempted path traversal attack blocked",
+            path=path,
+            url=url,
+            project=active_project.name,
+        )
+        return {
+            "type": "error",
+            "error": f"Path '{path}' is not allowed - paths must stay within project boundaries",
+        }
+
     response = await call_get(client, f"{project_url}/resource/{url}")
     content_type = response.headers.get("content-type", "application/octet-stream")
     content_length = int(response.headers.get("content-length", 0))

src/basic_memory/mcp/tools/read_note.py

@@ -11,6 +11,7 @@ from basic_memory.mcp.tools.search import search_notes
 from basic_memory.mcp.tools.utils import call_get
 from basic_memory.mcp.project_session import get_active_project
 from basic_memory.schemas.memory import memory_url_path
+from basic_memory.utils import validate_project_path
 
 
 @mcp.tool(
@@ -52,14 +53,31 @@ async def read_note(
         read_note("Meeting Notes", project="work-project")
     """
 
+    # 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
 
-    migration_status = await wait_for_migration_or_return_status(timeout=5.0)
+    migration_status = await wait_for_migration_or_return_status(
+        timeout=5.0, project_name=active_project.name
+    )
     if migration_status:  # pragma: no cover
         return f"# System Status\n\n{migration_status}\n\nPlease wait for migration to complete before reading notes."
-
-    active_project = get_active_project(project)
     project_url = active_project.project_url
 
     # Get the file via REST API - first try direct permalink lookup
@@ -121,7 +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
@@ -167,7 +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/mcp/tools/search.py

@@ -45,13 +45,18 @@ def _format_search_error_response(error_message: str, query: str, search_type: s
             - Boolean OR: `meeting OR discussion`
             - Boolean NOT: `project NOT archived`
             - Grouped: `(project OR planning) AND notes`
+            - Exact phrases: `"weekly standup meeting"`
+            - Content-specific: `tag:example` or `category:observation`
 
             ## Try again with:
             ```
-            search_notes("INSERT_CLEAN_QUERY_HERE")
+            search_notes("{clean_query}")
             ```
 
-            Replace INSERT_CLEAN_QUERY_HERE with your simplified search terms.
+            ## Alternative search strategies:
+            - Break into simpler terms: `search_notes("{" ".join(clean_query.split()[:2])}")`
+            - Try different search types: `search_notes("{clean_query}", search_type="title")`
+            - Use filtering: `search_notes("{clean_query}", types=["entity"])`
             """).strip()
 
     # Project not found errors (check before general "not found")
@@ -85,24 +90,39 @@ def _format_search_error_response(error_message: str, query: str, search_type: s
 
             No content found matching '{query}' in the current project.
 
-            ## Suggestions to try:
+            ## Search strategy suggestions:
             1. **Broaden your search**: Try fewer or more general terms
                - Instead of: `{query}`
                - Try: `{simplified_query}`
 
-            2. **Check spelling**: Verify terms are spelled correctly
-            3. **Try different search types**:
-               - Text search: `search_notes("{query}", search_type="text")`
-               - Title search: `search_notes("{query}", search_type="title")`
-               - Permalink search: `search_notes("{query}", search_type="permalink")`
+            2. **Check spelling and try variations**:
+               - Verify terms are spelled correctly
+               - Try synonyms or related terms
 
-            4. **Use boolean operators**:
-               - Try OR search for broader results
+            3. **Use different search approaches**:
+               - **Text search**: `search_notes("{query}", search_type="text")` (searches full content)
+               - **Title search**: `search_notes("{query}", search_type="title")` (searches only titles)
+               - **Permalink search**: `search_notes("{query}", search_type="permalink")` (searches file paths)
 
-            ## Check what content exists:
-            - Recent activity: `recent_activity(timeframe="7d")`
-            - List files: `list_directory("/")`
-            - Browse by folder: `list_directory("/notes")` or `list_directory("/docs")`
+            4. **Try boolean operators for broader results**:
+               - OR search: `search_notes("{" OR ".join(query.split()[:3])}")`
+               - Remove restrictive terms: Focus on the most important keywords
+
+            5. **Use filtering to narrow scope**:
+               - By content type: `search_notes("{query}", types=["entity"])`
+               - By recent content: `search_notes("{query}", after_date="1 week")`
+               - By entity type: `search_notes("{query}", entity_types=["observation"])`
+
+            6. **Try advanced search patterns**:
+               - Tag search: `search_notes("tag:your-tag")`
+               - Category search: `search_notes("category:observation")`
+               - Pattern matching: `search_notes("*{query}*", search_type="permalink")`
+
+            ## Explore what content exists:
+            - **Recent activity**: `recent_activity(timeframe="7d")` - See what's been updated recently
+            - **List directories**: `list_directory("/")` - Browse all content
+            - **Browse by folder**: `list_directory("/notes")` or `list_directory("/docs")`
+            - **Check project**: `get_current_project()` - Verify you're in the right project
             """).strip()
 
     # Server/API errors
@@ -151,25 +171,36 @@ You don't have permission to search in the current project: {error_message}
 
 Error searching for '{query}': {error_message}
 
-## General troubleshooting:
-1. **Check your query**: Ensure it uses valid search syntax
-2. **Try simpler terms**: Use basic words without special characters
+## Troubleshooting steps:
+1. **Simplify your query**: Try basic words without special characters
+2. **Check search syntax**: Ensure boolean operators are correctly formatted
 3. **Verify project access**: Make sure you can access the current project
-4. **Check recent activity**: `recent_activity(timeframe="7d")` to see if content exists
+4. **Test with simple search**: Try `search_notes("test")` to verify search is working
 
-## Alternative approaches:
-- Browse files: `list_directory("/")`
-- Try different search type: `search_notes("{query}", search_type="title")`
-- Search with filters: `search_notes("{query}", types=["entity"])`
+## Alternative search approaches:
+- **Different search types**: 
+  - Title only: `search_notes("{query}", search_type="title")`
+  - Permalink patterns: `search_notes("{query}*", search_type="permalink")`
+- **With filters**: `search_notes("{query}", types=["entity"])`
+- **Recent content**: `search_notes("{query}", after_date="1 week")`
+- **Boolean variations**: `search_notes("{" OR ".join(query.split()[:2])}")`
 
-## Need help?
-- View recent changes: `recent_activity()`
-- List projects: `list_projects()` 
-- Check current project: `get_current_project()`"""
+## Explore your content:
+- **Browse files**: `list_directory("/")` - See all available content
+- **Recent activity**: `recent_activity(timeframe="7d")` - Check what's been updated
+- **Project info**: `get_current_project()` - Verify current project
+- **All projects**: `list_projects()` - Switch to different project if needed
+
+## Search syntax reference:
+- **Basic**: `keyword` or `multiple words`
+- **Boolean**: `term1 AND term2`, `term1 OR term2`, `term1 NOT term2`
+- **Phrases**: `"exact phrase"`
+- **Grouping**: `(term1 OR term2) AND term3`
+- **Patterns**: `tag:example`, `category:observation`"""
 
 
 @mcp.tool(
-    description="Search across all content in the knowledge base.",
+    description="Search across all content in the knowledge base with advanced syntax support.",
 )
 async def search_notes(
     query: str,
@@ -181,24 +212,60 @@ async def search_notes(
     after_date: Optional[str] = None,
     project: Optional[str] = None,
 ) -> SearchResponse | str:
-    """Search across all content in the knowledge base.
+    """Search across all content in the knowledge base with comprehensive syntax support.
 
     This tool searches the knowledge base using full-text search, pattern matching,
     or exact permalink lookup. It supports filtering by content type, entity type,
-    and date.
+    and date, with advanced boolean and phrase search capabilities.
+
+    ## Search Syntax Examples
+
+    ### Basic Searches
+    - `search_notes("keyword")` - Find any content containing "keyword"
+    - `search_notes("exact phrase")` - Search for exact phrase match
+
+    ### Advanced Boolean Searches
+    - `search_notes("term1 term2")` - Find content with both terms (implicit AND)
+    - `search_notes("term1 AND term2")` - Explicit AND search (both terms required)
+    - `search_notes("term1 OR term2")` - Either term can be present
+    - `search_notes("term1 NOT term2")` - Include term1 but exclude term2
+    - `search_notes("(project OR planning) AND notes")` - Grouped boolean logic
+
+    ### Content-Specific Searches
+    - `search_notes("tag:example")` - Search within specific tags (if supported by content)
+    - `search_notes("category:observation")` - Filter by observation categories
+    - `search_notes("author:username")` - Find content by author (if metadata available)
+
+    ### Search Type Examples
+    - `search_notes("Meeting", search_type="title")` - Search only in titles
+    - `search_notes("docs/meeting-*", search_type="permalink")` - Pattern match permalinks
+    - `search_notes("keyword", search_type="text")` - Full-text search (default)
+
+    ### Filtering Options
+    - `search_notes("query", types=["entity"])` - Search only entities
+    - `search_notes("query", types=["note", "person"])` - Multiple content types
+    - `search_notes("query", entity_types=["observation"])` - Filter by entity type
+    - `search_notes("query", after_date="2024-01-01")` - Recent content only
+    - `search_notes("query", after_date="1 week")` - Relative date filtering
+
+    ### Advanced Pattern Examples
+    - `search_notes("project AND (meeting OR discussion)")` - Complex boolean logic
+    - `search_notes("\"exact phrase\" AND keyword")` - Combine phrase and keyword search
+    - `search_notes("bug NOT fixed")` - Exclude resolved issues
+    - `search_notes("docs/2024-*", search_type="permalink")` - Year-based permalink search
 
     Args:
-        query: The search query string
+        query: The search query string (supports boolean operators, phrases, patterns)
         page: The page number of results to return (default 1)
         page_size: The number of results to return per page (default 10)
         search_type: Type of search to perform, one of: "text", "title", "permalink" (default: "text")
         types: Optional list of note types to search (e.g., ["note", "person"])
         entity_types: Optional list of entity types to filter by (e.g., ["entity", "observation"])
-        after_date: Optional date filter for recent content (e.g., "1 week", "2d")
+        after_date: Optional date filter for recent content (e.g., "1 week", "2d", "2024-01-01")
         project: Optional project name to search in. If not provided, uses current active project.
 
     Returns:
-        SearchResponse with results and pagination info
+        SearchResponse with results and pagination info, or helpful error guidance if search fails
 
     Examples:
         # Basic text search
@@ -216,16 +283,19 @@ async def search_notes(
         # Boolean search with grouping
         results = await search_notes("(project OR planning) AND notes")
 
+        # Exact phrase search
+        results = await search_notes("\"weekly standup meeting\"")
+
         # Search with type filter
         results = await search_notes(
             query="meeting notes",
             types=["entity"],
         )
 
-        # Search with entity type filter, e.g., note vs
+        # Search with entity type filter
         results = await search_notes(
             query="meeting notes",
-            types=["entity"],
+            entity_types=["observation"],
         )
 
         # Search for recent content
@@ -242,6 +312,13 @@ async def search_notes(
 
         # Search in specific project
         results = await search_notes("meeting notes", project="work-project")
+
+        # Complex search with multiple filters
+        results = await search_notes(
+            query="(bug OR issue) AND NOT resolved",
+            types=["entity"],
+            after_date="2024-01-01"
+        )
     """
     # Create a SearchQuery object based on the parameters
     search_query = SearchQuery()

src/basic_memory/mcp/tools/sync_status.py

@@ -4,8 +4,10 @@ from typing import Optional
 
 from loguru import logger
 
+from basic_memory.config import ConfigManager
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.project_session import get_active_project
+from basic_memory.services.sync_status_service import sync_status_tracker
 
 
 def _get_all_projects_status() -> list[str]:
@@ -13,8 +15,7 @@ def _get_all_projects_status() -> list[str]:
     status_lines = []
 
     try:
-        from basic_memory.config import app_config
-        from basic_memory.services.sync_status_service import sync_status_tracker
+        app_config = ConfigManager().config
 
         if app_config.projects:
             status_lines.extend(["", "---", "", "**All Projects Status:**"])

src/basic_memory/mcp/tools/utils.py

@@ -525,11 +525,16 @@ def check_migration_status() -> Optional[str]:
         return None
 
 
-async def wait_for_migration_or_return_status(timeout: float = 5.0) -> Optional[str]:
+async def wait_for_migration_or_return_status(
+    timeout: float = 5.0, project_name: Optional[str] = None
+) -> Optional[str]:
     """Wait briefly for sync/migration to complete, or return status message.
 
     Args:
         timeout: Maximum time to wait for sync completion
+        project_name: Optional project name to check specific project status.
+                     If provided, only checks that project's readiness.
+                     If None, uses global status check (legacy behavior).
 
     Returns:
         Status message if sync is still in progress, None if ready
@@ -538,18 +543,36 @@ async def wait_for_migration_or_return_status(timeout: float = 5.0) -> Optional[
         from basic_memory.services.sync_status_service import sync_status_tracker
         import asyncio
 
-        if sync_status_tracker.is_ready:
+        # Check if we should use project-specific or global status
+        def is_ready() -> bool:
+            if project_name:
+                return sync_status_tracker.is_project_ready(project_name)
+            return sync_status_tracker.is_ready
+
+        if is_ready():
             return None
 
         # Wait briefly for sync to complete
         start_time = asyncio.get_event_loop().time()
         while (asyncio.get_event_loop().time() - start_time) < timeout:
-            if sync_status_tracker.is_ready:
+            if is_ready():
                 return None
             await asyncio.sleep(0.1)  # Check every 100ms
 
         # Still not ready after timeout
-        return sync_status_tracker.get_summary()
+        if project_name:
+            # For project-specific checks, get project status details
+            project_status = sync_status_tracker.get_project_status(project_name)
+            if project_status and project_status.status.value == "failed":
+                error_msg = project_status.error or "Unknown sync error"
+                return f"❌ Sync failed for project '{project_name}': {error_msg}"
+            elif project_status:
+                return f"🔄 Project '{project_name}' is still syncing: {project_status.message}"
+            else:
+                return f"⚠️ Project '{project_name}' status unknown"
+        else:
+            # Fall back to global summary for legacy calls
+            return sync_status_tracker.get_summary()
     except Exception:  # pragma: no cover
         # If there's any error, assume ready
         return None

src/basic_memory/mcp/tools/write_note.py

@@ -10,7 +10,7 @@ from basic_memory.mcp.tools.utils import call_put
 from basic_memory.mcp.project_session import get_active_project
 from basic_memory.schemas import EntityResponse
 from basic_memory.schemas.base import Entity
-from basic_memory.utils import parse_tags
+from basic_memory.utils import parse_tags, validate_project_path
 
 # Define TagType as a Union that can accept either a string or a list of strings or None
 TagType = Union[List[str], str, None]
@@ -72,10 +72,23 @@ async def write_note(
     """
     logger.info(f"MCP tool call tool=write_note folder={folder}, title={title}, tags={tags}")
 
+    # Get the active project first to check project-specific sync status
+    active_project = get_active_project(project)
+
+    # Validate folder path to prevent path traversal attacks
+    project_path = active_project.home
+    if folder and not validate_project_path(folder, project_path):
+        logger.warning(
+            "Attempted path traversal attack blocked", folder=folder, project=active_project.name
+        )
+        return f"# Error\n\nFolder path '{folder}' is not allowed - paths must stay within project boundaries"
+
     # Check migration status and wait briefly if needed
     from basic_memory.mcp.tools.utils import wait_for_migration_or_return_status
 
-    migration_status = await wait_for_migration_or_return_status(timeout=5.0)
+    migration_status = await wait_for_migration_or_return_status(
+        timeout=5.0, project_name=active_project.name
+    )
     if migration_status:  # pragma: no cover
         return f"# System Status\n\n{migration_status}\n\nPlease wait for migration to complete before creating notes."
 
@@ -91,7 +104,6 @@ async def write_note(
         content=content,
         entity_metadata=metadata,
     )
-    active_project = get_active_project(project)
     project_url = active_project.project_url
 
     # Create or update via knowledge API

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

@@ -1,6 +1,6 @@
 """Project model for Basic Memory."""
 
-from datetime import datetime
+from datetime import datetime, UTC
 from typing import Optional
 
 from sqlalchemy import (
@@ -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=datetime.utcnow)
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
     updated_at: Mapped[datetime] = mapped_column(
-        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow
+        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."""
@@ -142,7 +142,7 @@ class EntityRepository(Repository[Entity]):
                 await session.flush()
                 # Return with relationships loaded
                 query = (
-                    select(Entity)
+                    self.select()
                     .where(Entity.file_path == entity.file_path)
                     .options(*self.get_load_options())
                 )
@@ -162,7 +162,7 @@ class EntityRepository(Repository[Entity]):
 
                 # Return with relationships loaded
                 query = (
-                    select(Entity)
+                    self.select()
                     .where(Entity.file_path == entity.file_path)
                     .options(*self.get_load_options())
                 )
@@ -203,7 +203,7 @@ class EntityRepository(Repository[Entity]):
                     await session.flush()
                     # Return the updated entity with relationships loaded
                     query = (
-                        select(Entity)
+                        self.select()
                         .where(Entity.file_path == entity.file_path)
                         .options(*self.get_load_options())
                     )
@@ -243,7 +243,7 @@ class EntityRepository(Repository[Entity]):
 
         # Return the inserted entity with relationships loaded
         query = (
-            select(Entity)
+            self.select()
             .where(Entity.file_path == entity.file_path)
             .options(*self.get_load_options())
         )

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]:
@@ -83,3 +83,21 @@ class ProjectRepository(Repository[Project]):
                 await session.flush()
                 return target_project
             return None  # pragma: no cover
+
+    async def update_path(self, project_id: int, new_path: str) -> Optional[Project]:
+        """Update project path.
+
+        Args:
+            project_id: ID of the project to update
+            new_path: New filesystem path for the project
+
+        Returns:
+            The updated project if found, None otherwise
+        """
+        async with db.scoped_session(self.session_maker) as session:
+            project = await self.select_by_id(session, project_id)
+            if project:
+                project.path = new_path
+                await session.flush()
+                return project
+            return None

src/basic_memory/repository/search_repository.py

@@ -1,10 +1,12 @@
 """Repository for search operations."""
 
 import json
+import re
 import time
 from dataclasses import dataclass
 from datetime import datetime
 from typing import Any, Dict, List, Optional
+from pathlib import Path
 
 from loguru import logger
 from sqlalchemy import Executable, Result, text
@@ -58,8 +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:
@@ -120,23 +125,141 @@ class SearchRepository:
             logger.error(f"Error initializing search index: {e}")
             raise e
 
-    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
-        """Prepare a search term for FTS5 query.
+    def _prepare_boolean_query(self, query: str) -> str:
+        """Prepare a Boolean query by quoting individual terms while preserving operators.
 
         Args:
-            term: The search term to prepare
+            query: A Boolean query like "tier1-test AND unicode" or "(hello OR world) NOT test"
+
+        Returns:
+            A properly formatted Boolean query with quoted terms that need quoting
+        """
+        # Define Boolean operators and their boundaries
+        boolean_pattern = r"(\bAND\b|\bOR\b|\bNOT\b)"
+
+        # Split the query by Boolean operators, keeping the operators
+        parts = re.split(boolean_pattern, query)
+
+        processed_parts = []
+        for part in parts:
+            part = part.strip()
+            if not part:
+                continue
+
+            # If it's a Boolean operator, keep it as is
+            if part in ["AND", "OR", "NOT"]:
+                processed_parts.append(part)
+            else:
+                # Handle parentheses specially - they should be preserved for grouping
+                if "(" in part or ")" in part:
+                    # Parse parenthetical expressions carefully
+                    processed_part = self._prepare_parenthetical_term(part)
+                    processed_parts.append(processed_part)
+                else:
+                    # This is a search term - for Boolean queries, don't add prefix wildcards
+                    prepared_term = self._prepare_single_term(part, is_prefix=False)
+                    processed_parts.append(prepared_term)
+
+        return " ".join(processed_parts)
+
+    def _prepare_parenthetical_term(self, term: str) -> str:
+        """Prepare a term that contains parentheses, preserving the parentheses for grouping.
+
+        Args:
+            term: A term that may contain parentheses like "(hello" or "world)" or "(hello OR world)"
+
+        Returns:
+            A properly formatted term with parentheses preserved
+        """
+        # Handle terms that start/end with parentheses but may contain quotable content
+        result = ""
+        i = 0
+        while i < len(term):
+            if term[i] in "()":
+                # Preserve parentheses as-is
+                result += term[i]
+                i += 1
+            else:
+                # Find the next parenthesis or end of string
+                start = i
+                while i < len(term) and term[i] not in "()":
+                    i += 1
+
+                # Extract the content between parentheses
+                content = term[start:i].strip()
+                if content:
+                    # Only quote if it actually needs quoting (has hyphens, special chars, etc)
+                    # but don't quote if it's just simple words
+                    if self._needs_quoting(content):
+                        escaped_content = content.replace('"', '""')
+                        result += f'"{escaped_content}"'
+                    else:
+                        result += content
+
+        return result
+
+    def _needs_quoting(self, term: str) -> bool:
+        """Check if a term needs to be quoted for FTS5 safety.
+
+        Args:
+            term: The term to check
+
+        Returns:
+            True if the term should be quoted
+        """
+        if not term or not term.strip():
+            return False
+
+        # Characters that indicate we should quote (excluding parentheses which are valid syntax)
+        needs_quoting_chars = [
+            " ",
+            ".",
+            ":",
+            ";",
+            ",",
+            "<",
+            ">",
+            "?",
+            "/",
+            "-",
+            "'",
+            '"',
+            "[",
+            "]",
+            "{",
+            "}",
+            "+",
+            "!",
+            "@",
+            "#",
+            "$",
+            "%",
+            "^",
+            "&",
+            "=",
+            "|",
+            "\\",
+            "~",
+            "`",
+        ]
+
+        return any(c in term for c in needs_quoting_chars)
+
+    def _prepare_single_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a single search term (no Boolean operators).
+
+        Args:
+            term: A single search term
             is_prefix: Whether to add prefix search capability (* suffix)
 
-        For FTS5:
-        - Boolean operators (AND, OR, NOT) are preserved for complex queries
-        - Terms with FTS5 special characters are quoted to prevent syntax errors
-        - Simple terms get prefix wildcards for better matching
+        Returns:
+            A properly formatted single term
         """
-        # Check for explicit boolean operators - if present, return the term as is
-        boolean_operators = [" AND ", " OR ", " NOT "]
-        if any(op in f" {term} " for op in boolean_operators):
+        if not term or not term.strip():
             return term
 
+        term = term.strip()
+
         # Check if term is already a proper wildcard pattern (alphanumeric + *)
         # e.g., "hello*", "test*world" - these should be left alone
         if "*" in term and all(c.isalnum() or c in "*_-" for c in term):
@@ -218,6 +341,26 @@ class SearchRepository:
 
         return term
 
+    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a search term for FTS5 query.
+
+        Args:
+            term: The search term to prepare
+            is_prefix: Whether to add prefix search capability (* suffix)
+
+        For FTS5:
+        - Boolean operators (AND, OR, NOT) are preserved for complex queries
+        - Terms with FTS5 special characters are quoted to prevent syntax errors
+        - Simple terms get prefix wildcards for better matching
+        """
+        # Check for explicit boolean operators - if present, process as Boolean query
+        boolean_operators = [" AND ", " OR ", " NOT "]
+        if any(op in f" {term} " for op in boolean_operators):
+            return self._prepare_boolean_query(term)
+
+        # For non-Boolean queries, use the single term preparation logic
+        return self._prepare_single_term(term, is_prefix)
+
     async def search(
         self,
         search_text: Optional[str] = None,
@@ -242,19 +385,10 @@ class SearchRepository:
                 # For wildcard searches, don't add any text conditions - return all results
                 pass
             else:
-                # Check for explicit boolean operators - only detect them in proper boolean contexts
-                has_boolean = any(op in f" {search_text} " for op in [" AND ", " OR ", " NOT "])
-
-                if has_boolean:
-                    # If boolean operators are present, use the raw query
-                    # No need to prepare it, FTS5 will understand the operators
-                    params["text"] = search_text
-                    conditions.append("(title MATCH :text OR content_stems MATCH :text)")
-                else:
-                    # Standard search with term preparation
-                    processed_text = self._prepare_search_term(search_text.strip())
-                    params["text"] = processed_text
-                    conditions.append("(title MATCH :text OR content_stems MATCH :text)")
+                # Use _prepare_search_term to handle both Boolean and non-Boolean queries
+                processed_text = self._prepare_search_term(search_text.strip())
+                params["text"] = processed_text
+                conditions.append("(title MATCH :text OR content_stems MATCH :text)")
 
         # Handle title match search
         if title:
@@ -393,8 +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/importer.py

@@ -32,3 +32,4 @@ class EntityImportResult(ImportResult):
 
     entities: int = 0
     relations: int = 0
+    skipped_entities: int = 0

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
@@ -128,21 +130,25 @@ 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
     relation_type: str
-    from_entity: str
+    from_entity: Optional[str] = None
     to_entity: Optional[str] = None
     created_at: datetime
 
 
 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/schemas/response.py

@@ -131,7 +131,7 @@ class EntityResponse(SQLAlchemyModel):
     }
     """
 
-    permalink: Permalink
+    permalink: Optional[Permalink]
     title: str
     file_path: str
     entity_type: EntityType

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

@@ -9,12 +9,13 @@ 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
 from basic_memory.models import Entity as EntityModel
 from basic_memory.models import Observation, Relation
+from basic_memory.models.knowledge import Entity
 from basic_memory.repository import ObservationRepository, RelationRepository
 from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.schemas import Entity as EntitySchema
@@ -44,6 +45,39 @@ class EntityService(BaseService[EntityModel]):
         self.file_service = file_service
         self.link_resolver = link_resolver
 
+    async def detect_file_path_conflicts(self, file_path: str) -> List[Entity]:
+        """Detect potential file path conflicts for a given file path.
+
+        This checks for entities with similar file paths that might cause conflicts:
+        - Case sensitivity differences (Finance/file.md vs finance/file.md)
+        - Character encoding differences
+        - Hyphen vs space differences
+        - Unicode normalization differences
+
+        Args:
+            file_path: The file path to check for conflicts
+
+        Returns:
+            List of entities that might conflict with the given file path
+        """
+        from basic_memory.utils import detect_potential_file_conflicts
+
+        conflicts = []
+
+        # Get all existing file paths
+        all_entities = await self.repository.find_all()
+        existing_paths = [entity.file_path for entity in all_entities]
+
+        # Use the enhanced conflict detection utility
+        conflicting_paths = detect_potential_file_conflicts(file_path, existing_paths)
+
+        # Find the entities corresponding to conflicting paths
+        for entity in all_entities:
+            if entity.file_path in conflicting_paths:
+                conflicts.append(entity)
+
+        return conflicts
+
     async def resolve_permalink(
         self, file_path: Permalink | Path, markdown: Optional[EntityMarkdown] = None
     ) -> str:
@@ -54,18 +88,30 @@ class EntityService(BaseService[EntityModel]):
         2. If markdown has permalink but it's used by another file -> make unique
         3. For existing files, keep current permalink from db
         4. Generate new unique permalink from file path
+
+        Enhanced to detect and handle character-related conflicts.
         """
+        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)
+        if conflicts:
+            logger.warning(
+                f"Detected potential file path conflicts for '{file_path_str}': "
+                f"{[entity.file_path for entity in conflicts]}"
+            )
+
         # If markdown has explicit permalink, try to validate it
         if markdown and markdown.frontmatter.permalink:
             desired_permalink = markdown.frontmatter.permalink
             existing = await self.repository.get_by_permalink(desired_permalink)
 
             # If no conflict or it's our own file, use as is
-            if not existing or existing.file_path == str(file_path):
+            if not existing or existing.file_path == file_path_str:
                 return desired_permalink
 
         # For existing files, try to find current permalink
-        existing = await self.repository.get_by_file_path(str(file_path))
+        existing = await self.repository.get_by_file_path(file_path_str)
         if existing:
             return existing.permalink
 
@@ -73,9 +119,9 @@ 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
+        # Make unique if needed - enhanced to handle character conflicts
         permalink = desired_permalink
         suffix = 1
         while await self.repository.get_by_permalink(permalink):
@@ -150,7 +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
@@ -227,7 +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
@@ -237,7 +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})
@@ -328,7 +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)
@@ -452,7 +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})
@@ -682,8 +728,8 @@ class EntityService(BaseService[EntityModel]):
             # 6. Prepare database updates
             updates = {"file_path": destination_path}
 
-            # 7. Update permalink if configured
-            if app_config.update_permalinks_on_move:
+            # 7. Update permalink if configured or if entity has null permalink
+            if app_config.update_permalinks_on_move or old_permalink is None:
                 # Generate new permalink from destination path
                 new_permalink = await self.resolve_permalink(destination_path)
 
@@ -693,7 +739,12 @@ class EntityService(BaseService[EntityModel]):
                 )
 
                 updates["permalink"] = new_permalink
-                logger.info(f"Updated permalink: {old_permalink} -> {new_permalink}")
+                if old_permalink is None:
+                    logger.info(
+                        f"Generated permalink for entity with null permalink: {new_permalink}"
+                    )
+                else:
+                    logger.info(f"Updated permalink: {old_permalink} -> {new_permalink}")
 
             # 8. Recalculate checksum
             new_checksum = await self.file_service.compute_checksum(destination_path)

src/basic_memory/services/initialization.py

@@ -5,14 +5,12 @@ to ensure consistent application startup across all entry points.
 """
 
 import asyncio
-import shutil
 from pathlib import Path
 
 from loguru import logger
 
 from basic_memory import db
 from basic_memory.config import BasicMemoryConfig
-from basic_memory.models import Project
 from basic_memory.repository import ProjectRepository
 
 
@@ -70,63 +68,6 @@ async def reconcile_projects_with_config(app_config: BasicMemoryConfig):
         logger.info("Continuing with initialization despite synchronization error")
 
 
-async def migrate_legacy_projects(app_config: BasicMemoryConfig):
-    # Get database session - migrations handled centrally
-    _, session_maker = await db.get_or_create_db(
-        db_path=app_config.database_path,
-        db_type=db.DatabaseType.FILESYSTEM,
-        ensure_migrations=False,
-    )
-    logger.info("Migrating legacy projects...")
-    project_repository = ProjectRepository(session_maker)
-
-    # For each project in config.json, check if it has a .basic-memory dir
-    for project_name, project_path in app_config.projects.items():
-        legacy_dir = Path(project_path) / ".basic-memory"
-        if not legacy_dir.exists():
-            continue
-        logger.info(f"Detected legacy project directory: {legacy_dir}")
-        project = await project_repository.get_by_name(project_name)
-        if not project:  # pragma: no cover
-            logger.error(f"Project {project_name} not found in database, skipping migration")
-            continue
-
-        logger.info(f"Starting migration for project: {project_name} (id: {project.id})")
-        await migrate_legacy_project_data(project, legacy_dir)
-        logger.info(f"Completed migration for project: {project_name}")
-    logger.info("Legacy projects successfully migrated")
-
-
-async def migrate_legacy_project_data(project: Project, legacy_dir: Path) -> bool:
-    """Check if project has legacy .basic-memory dir and migrate if needed.
-
-    Args:
-        project: The project to check and potentially migrate
-
-    Returns:
-        True if migration occurred, False otherwise
-    """
-
-    # avoid circular imports
-    from basic_memory.cli.commands.sync import get_sync_service
-
-    sync_service = await get_sync_service(project)
-    sync_dir = Path(project.path)
-
-    logger.info(f"Sync starting project: {project.name}")
-    await sync_service.sync(sync_dir, project_name=project.name)
-    logger.info(f"Sync completed successfully for project: {project.name}")
-
-    # After successful sync, remove the legacy directory
-    try:
-        logger.info(f"Removing legacy directory: {legacy_dir}")
-        shutil.rmtree(legacy_dir)
-        return True
-    except Exception as e:
-        logger.error(f"Error removing legacy directory: {e}")
-        return False
-
-
 async def initialize_file_sync(
     app_config: BasicMemoryConfig,
 ):
@@ -186,16 +127,6 @@ async def initialize_file_sync(
             sync_status_tracker.fail_project_sync(project.name, str(e))
             # Continue with other projects even if one fails
 
-    # Mark migration complete if it was in progress
-    try:
-        from basic_memory.services.migration_service import migration_manager
-
-        if not migration_manager.is_ready:  # pragma: no cover
-            migration_manager.mark_completed("Migration completed with file sync")
-            logger.info("Marked migration as completed after file sync")
-    except Exception as e:  # pragma: no cover
-        logger.warning(f"Could not update migration status: {e}")
-
     # Then start the watch service in the background
     logger.info("Starting watch service for all projects")
     # run the watch service
@@ -229,13 +160,7 @@ async def initialize_app(
     # Reconcile projects from config.json with projects table
     await reconcile_projects_with_config(app_config)
 
-    # Start background migration for legacy project data (non-blocking)
-    from basic_memory.services.migration_service import migration_manager
-
-    await migration_manager.start_background_migration(app_config)
-
     logger.info("App initialization completed (migration running in background if needed)")
-    return migration_manager
 
 
 def ensure_initialization(app_config: BasicMemoryConfig) -> None:

src/basic_memory/services/migration_service.py

@@ -1,168 +0,0 @@
-"""Migration service for handling background migrations and status tracking."""
-
-import asyncio
-from dataclasses import dataclass
-from enum import Enum
-from pathlib import Path
-from typing import Optional
-
-from loguru import logger
-
-from basic_memory.config import BasicMemoryConfig
-
-
-class MigrationStatus(Enum):
-    """Status of migration operations."""
-
-    NOT_NEEDED = "not_needed"
-    PENDING = "pending"
-    IN_PROGRESS = "in_progress"
-    COMPLETED = "completed"
-    FAILED = "failed"
-
-
-@dataclass
-class MigrationState:
-    """Current state of migration operations."""
-
-    status: MigrationStatus
-    message: str
-    progress: Optional[str] = None
-    error: Optional[str] = None
-    projects_migrated: int = 0
-    projects_total: int = 0
-
-
-class MigrationManager:
-    """Manages background migration operations and status tracking."""
-
-    def __init__(self):
-        self._state = MigrationState(
-            status=MigrationStatus.NOT_NEEDED, message="No migration required"
-        )
-        self._migration_task: Optional[asyncio.Task] = None
-
-    @property
-    def state(self) -> MigrationState:
-        """Get current migration state."""
-        return self._state
-
-    @property
-    def is_ready(self) -> bool:
-        """Check if the system is ready for normal operations."""
-        return self._state.status in (MigrationStatus.NOT_NEEDED, MigrationStatus.COMPLETED)
-
-    @property
-    def status_message(self) -> str:
-        """Get a user-friendly status message."""
-        if self._state.status == MigrationStatus.IN_PROGRESS:
-            progress = (
-                f" ({self._state.projects_migrated}/{self._state.projects_total})"
-                if self._state.projects_total > 0
-                else ""
-            )
-            return f"🔄 File sync in progress{progress}: {self._state.message}. Use sync_status() tool for details."
-        elif self._state.status == MigrationStatus.FAILED:
-            return f"❌ File sync failed: {self._state.error or 'Unknown error'}. Use sync_status() tool for details."
-        elif self._state.status == MigrationStatus.COMPLETED:
-            return "✅ File sync completed successfully"
-        else:
-            return "✅ System ready"
-
-    async def check_migration_needed(self, app_config: BasicMemoryConfig) -> bool:
-        """Check if migration is needed without performing it."""
-        from basic_memory import db
-        from basic_memory.repository import ProjectRepository
-
-        try:
-            # Get database session
-            _, session_maker = await db.get_or_create_db(
-                db_path=app_config.database_path, db_type=db.DatabaseType.FILESYSTEM
-            )
-            project_repository = ProjectRepository(session_maker)
-
-            # Check for legacy projects
-            legacy_projects = []
-            for project_name, project_path in app_config.projects.items():
-                legacy_dir = Path(project_path) / ".basic-memory"
-                if legacy_dir.exists():
-                    project = await project_repository.get_by_name(project_name)
-                    if project:
-                        legacy_projects.append(project)
-
-            if legacy_projects:
-                self._state = MigrationState(
-                    status=MigrationStatus.PENDING,
-                    message="Legacy projects detected",
-                    projects_total=len(legacy_projects),
-                )
-                return True
-            else:
-                self._state = MigrationState(
-                    status=MigrationStatus.NOT_NEEDED, message="No migration required"
-                )
-                return False
-
-        except Exception as e:
-            logger.error(f"Error checking migration status: {e}")
-            self._state = MigrationState(
-                status=MigrationStatus.FAILED, message="Migration check failed", error=str(e)
-            )
-            return False
-
-    async def start_background_migration(self, app_config: BasicMemoryConfig) -> None:
-        """Start migration in background if needed."""
-        if not await self.check_migration_needed(app_config):
-            return
-
-        if self._migration_task and not self._migration_task.done():
-            logger.info("Migration already in progress")
-            return
-
-        logger.info("Starting background migration")
-        self._migration_task = asyncio.create_task(self._run_migration(app_config))
-
-    async def _run_migration(self, app_config: BasicMemoryConfig) -> None:
-        """Run the actual migration process."""
-        try:
-            self._state.status = MigrationStatus.IN_PROGRESS
-            self._state.message = "Migrating legacy projects"
-
-            # Import here to avoid circular imports
-            from basic_memory.services.initialization import migrate_legacy_projects
-
-            # Run the migration
-            await migrate_legacy_projects(app_config)
-
-            self._state = MigrationState(
-                status=MigrationStatus.COMPLETED, message="Migration completed successfully"
-            )
-            logger.info("Background migration completed successfully")
-
-        except Exception as e:
-            logger.error(f"Background migration failed: {e}")
-            self._state = MigrationState(
-                status=MigrationStatus.FAILED, message="Migration failed", error=str(e)
-            )
-
-    async def wait_for_completion(self, timeout: Optional[float] = None) -> bool:
-        """Wait for migration to complete."""
-        if self.is_ready:
-            return True
-
-        if not self._migration_task:
-            return False
-
-        try:
-            await asyncio.wait_for(self._migration_task, timeout=timeout)
-            return self.is_ready
-        except asyncio.TimeoutError:
-            return False
-
-    def mark_completed(self, message: str = "Migration completed") -> None:
-        """Mark migration as completed externally."""
-        self._state = MigrationState(status=MigrationStatus.COMPLETED, message=message)
-
-
-# Global migration manager instance
-migration_manager = MigrationManager()

src/basic_memory/services/project_service.py

@@ -9,7 +9,6 @@ from typing import Dict, Optional, Sequence
 from loguru import logger
 from sqlalchemy import text
 
-from basic_memory.config import config, app_config
 from basic_memory.models import Project
 from basic_memory.repository.project_repository import ProjectRepository
 from basic_memory.schemas import (
@@ -18,9 +17,8 @@ from basic_memory.schemas import (
     ProjectStatistics,
     SystemStatus,
 )
-from basic_memory.config import WATCH_STATUS_JSON
+from basic_memory.config import WATCH_STATUS_JSON, ConfigManager, get_project_config, ProjectConfig
 from basic_memory.utils import generate_permalink
-from basic_memory.config import config_manager
 
 
 class ProjectService:
@@ -33,6 +31,24 @@ class ProjectService:
         super().__init__()
         self.repository = repository
 
+    @property
+    def config_manager(self) -> ConfigManager:
+        """Get a ConfigManager instance.
+
+        Returns:
+            Fresh ConfigManager instance for each access
+        """
+        return ConfigManager()
+
+    @property
+    def config(self) -> ProjectConfig:
+        """Get the current project configuration.
+
+        Returns:
+            Current project configuration
+        """
+        return get_project_config()
+
     @property
     def projects(self) -> Dict[str, str]:
         """Get all configured projects.
@@ -40,7 +56,7 @@ class ProjectService:
         Returns:
             Dict mapping project names to their file paths
         """
-        return config_manager.projects
+        return self.config_manager.projects
 
     @property
     def default_project(self) -> str:
@@ -49,7 +65,7 @@ class ProjectService:
         Returns:
             The name of the default project
         """
-        return config_manager.default_project
+        return self.config_manager.default_project
 
     @property
     def current_project(self) -> str:
@@ -58,7 +74,7 @@ class ProjectService:
         Returns:
             The name of the current project
         """
-        return os.environ.get("BASIC_MEMORY_PROJECT", config_manager.default_project)
+        return os.environ.get("BASIC_MEMORY_PROJECT", self.config_manager.default_project)
 
     async def list_projects(self) -> Sequence[Project]:
         return await self.repository.find_all()
@@ -84,10 +100,10 @@ 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 = config_manager.add_project(name, resolved_path)
+        project_config = self.config_manager.add_project(name, resolved_path)
 
         # Then add to database
         project_data = {
@@ -103,7 +119,7 @@ class ProjectService:
         # If this should be the default project, ensure only one default exists
         if set_default:
             await self.repository.set_as_default(created_project.id)
-            config_manager.set_default_project(name)
+            self.config_manager.set_default_project(name)
             logger.info(f"Project '{name}' set as default")
 
         logger.info(f"Project '{name}' added at {resolved_path}")
@@ -121,10 +137,10 @@ class ProjectService:
             raise ValueError("Repository is required for remove_project")
 
         # First remove from config (this will validate the project exists and is not default)
-        config_manager.remove_project(name)
+        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)
 
@@ -143,10 +159,10 @@ class ProjectService:
             raise ValueError("Repository is required for set_default_project")
 
         # First update config file (this will validate the project exists)
-        config_manager.set_default_project(name)
+        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:
@@ -196,7 +212,7 @@ class ProjectService:
         elif len(default_projects) == 0:  # pragma: no cover
             # No default project - set the config default as default
             # This is defensive code for edge cases where no default exists
-            config_default = config_manager.default_project  # pragma: no cover
+            config_default = self.config_manager.default_project  # pragma: no cover
             config_project = await self.repository.get_by_name(config_default)  # pragma: no cover
             if config_project:  # pragma: no cover
                 await self.repository.set_as_default(config_project.id)  # pragma: no cover
@@ -221,7 +237,7 @@ class ProjectService:
         db_projects_by_permalink = {p.permalink: p for p in db_projects}
 
         # Get all projects from configuration and normalize names if needed
-        config_projects = config_manager.projects.copy()
+        config_projects = self.config_manager.projects.copy()
         updated_config = {}
         config_updated = False
 
@@ -237,8 +253,9 @@ class ProjectService:
 
         # Update the configuration if any changes were made
         if config_updated:
-            config_manager.config.projects = updated_config
-            config_manager.save_config(config_manager.config)
+            config = self.config_manager.load_config()
+            config.projects = updated_config
+            self.config_manager.save_config(config)
             logger.info("Config updated with normalized project names")
 
         # Use the normalized config for further processing
@@ -261,19 +278,19 @@ class ProjectService:
         for name, project in db_projects_by_permalink.items():
             if name not in config_projects:
                 logger.info(f"Adding project '{name}' to configuration")
-                config_manager.add_project(name, project.path)
+                self.config_manager.add_project(name, project.path)
 
         # Ensure database default project state is consistent
         await self._ensure_single_default_project()
 
         # Make sure default project is synchronized between config and database
         db_default = await self.repository.get_default_project()
-        config_default = config_manager.default_project
+        config_default = self.config_manager.default_project
 
         if db_default and db_default.name != config_default:
             # Update config to match DB default
             logger.info(f"Updating default project in config to '{db_default.name}'")
-            config_manager.set_default_project(db_default.name)
+            self.config_manager.set_default_project(db_default.name)
         elif not db_default and config_default:
             # Update DB to match config default (if the project exists)
             project = await self.repository.get_by_name(config_default)
@@ -292,6 +309,47 @@ class ProjectService:
             # MCP components might not be available in all contexts
             logger.debug("MCP session not available, skipping session refresh")
 
+    async def move_project(self, name: str, new_path: str) -> None:
+        """Move a project to a new location.
+
+        Args:
+            name: The name of the project to move
+            new_path: The new absolute path for the project
+
+        Raises:
+            ValueError: If the project doesn't exist or repository isn't initialized
+        """
+        if not self.repository:
+            raise ValueError("Repository is required for move_project")
+
+        # Resolve to absolute 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:
+            raise ValueError(f"Project '{name}' not found in configuration")
+
+        # Create the new directory if it doesn't exist
+        Path(resolved_path).mkdir(parents=True, exist_ok=True)
+
+        # Update in configuration
+        config = self.config_manager.load_config()
+        old_path = config.projects[name]
+        config.projects[name] = resolved_path
+        self.config_manager.save_config(config)
+
+        # 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}")
+        else:
+            logger.error(f"Project '{name}' exists in config but not in database")
+            # Restore the old path in config since DB update failed
+            config.projects[name] = old_path
+            self.config_manager.save_config(config)
+            raise ValueError(f"Project '{name}' not found in database")
+
     async def update_project(  # pragma: no cover
         self, name: str, updated_path: Optional[str] = None, is_active: Optional[bool] = None
     ) -> None:
@@ -309,24 +367,23 @@ class ProjectService:
             raise ValueError("Repository is required for update_project")
 
         # Validate project exists in config
-        if name not in config_manager.projects:
+        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
-            projects = config_manager.config.projects.copy()
-            projects[name] = resolved_path
-            config_manager.config.projects = projects
-            config_manager.save_config(config_manager.config)
+            config = self.config_manager.load_config()
+            config.projects[name] = resolved_path
+            self.config_manager.save_config(config)
 
             # Update in database
             project.path = resolved_path
@@ -347,7 +404,7 @@ class ProjectService:
             if active_projects:
                 new_default = active_projects[0]
                 await self.repository.set_as_default(new_default.id)
-                config_manager.set_default_project(new_default.name)
+                self.config_manager.set_default_project(new_default.name)
                 logger.info(
                     f"Changed default project to '{new_default.name}' as '{name}' was deactivated"
                 )
@@ -365,9 +422,9 @@ class ProjectService:
             raise ValueError("Repository is required for get_project_info")
 
         # Use specified project or fall back to config project
-        project_name = project_name or config.project
+        project_name = project_name or self.config.project
         # Get project path from configuration
-        name, project_path = config_manager.get_project(project_name)
+        name, project_path = self.config_manager.get_project(project_name)
         if not name:  # pragma: no cover
             raise ValueError(f"Project '{project_name}' not found in configuration")
 
@@ -393,11 +450,11 @@ class ProjectService:
         db_projects_by_permalink = {p.permalink: p for p in db_projects}
 
         # Get default project info
-        default_project = config_manager.default_project
+        default_project = self.config_manager.default_project
 
         # Convert config projects to include database info
         enhanced_projects = {}
-        for name, path in config_manager.projects.items():
+        for name, path in self.config_manager.projects.items():
             config_permalink = generate_permalink(name)
             db_project = db_projects_by_permalink.get(config_permalink)
             enhanced_projects[name] = {
@@ -673,7 +730,7 @@ class ProjectService:
         import basic_memory
 
         # Get database information
-        db_path = app_config.database_path
+        db_path = self.config_manager.config.database_path
         db_size = db_path.stat().st_size if db_path.exists() else 0
         db_size_readable = f"{db_size / (1024 * 1024):.2f} MB"
 

src/basic_memory/services/sync_status_service.py

@@ -131,6 +131,23 @@ class SyncStatusTracker:
         """Check if system is ready (no sync in progress)."""
         return self._global_status in (SyncStatus.IDLE, SyncStatus.COMPLETED)
 
+    def is_project_ready(self, project_name: str) -> bool:
+        """Check if a specific project is ready for operations.
+
+        Args:
+            project_name: Name of the project to check
+
+        Returns:
+            True if the project is ready (completed, watching, or not tracked),
+            False if the project is syncing, scanning, or failed
+        """
+        project_status = self._project_statuses.get(project_name)
+        if not project_status:
+            # Project not tracked = ready (likely hasn't been synced yet)
+            return True
+
+        return project_status.status in (SyncStatus.COMPLETED, SyncStatus.WATCHING, SyncStatus.IDLE)
+
     def get_project_status(self, project_name: str) -> Optional[ProjectSyncStatus]:
         """Get status for a specific project."""
         return self._project_statuses.get(project_name)