Denormalizes project_id onto Relation and Observation tables to enable
efficient project-scoped queries without joins. Migration backfills
from associated entity and adds pg_trgm extension with GIN indexes
for fuzzy link resolution on PostgreSQL.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>
Add optimized repository methods for resolve_permalink() that skip
eager loading of observations and relations:
- permalink_exists(): Check existence without loading entity
- get_file_path_for_permalink(): Get only file_path column
- get_permalink_for_file_path(): Get only permalink column
- get_all_permalinks(): Get all permalinks as strings
- get_permalink_to_file_path_map(): Bulk lookup mapping
- get_file_path_to_permalink_map(): Reverse mapping
Updated entity_service.resolve_permalink() to use these lightweight
methods instead of loading full entities with all relationships.
Also added logfire instrumentation to markdown utils.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>
Fixes critical data loss bug where creating similar entity names
(e.g., "Node C") would overwrite existing entities (e.g., "Node A.md")
due to fuzzy search incorrectly matching similar file paths.
Changes:
- Add strict=True to resolve_link() calls in entity_service.py
- Disables fuzzy search fallback during entity creation/update
- Prevents false positive matches on similar paths like
"edge-cases/Node A.md" and "edge-cases/Node C.md"
Testing:
- Added comprehensive integration test reproducing the bug scenario
- Added MCP-level permalink collision tests
- All 55 entity service tests pass
- Manual testing confirms fix prevents file overwrite
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>
Fixes#36 by modifying entity_service.update_entity() to read existing
frontmatter from files before updating them. Custom metadata fields
such as Status, Priority, and Version are now preserved when notes
are updated through the write_note MCP tool.
Added test case that verifies this behavior by creating a note with
custom frontmatter and then updating it.
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>
Fixes#36 by modifying entity_service.update_entity() to read existing
frontmatter from files before updating them. Custom metadata fields
such as Status, Priority, and Version are now preserved when notes
are updated through the write_note MCP tool.
Added test case that verifies this behavior by creating a note with
custom frontmatter and then updating it.
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
feat: Add multiple projects support
feat: enhanced read_note for when initial result is not found
fix: merge frontmatter when updating note
fix: handle directory removed on sync watch
## Summary
- Add comprehensive documentation to all MCP prompt modules
- Enhance search prompt with detailed contextual output formatting
- Implement consistent logging and docstring patterns across prompt
utilities
- Fix type checking in prompt modules
## Prompts Added/Enhanced
- `search.py`: New formatted output with relevance scores, excerpts, and
next steps
- `recent_activity.py`: Enhanced with better metadata handling and
documentation
- `continue_conversation.py`: Improved context management
## Resources Added/Enhanced
- `ai_assistant_guide`: Resource with description to give to LLM to
understand how to use the tools
## Technical improvements
- Added detailed docstrings to all prompt modules explaining their
purpose and usage
- Enhanced the search prompt with rich contextual output that helps LLMs
understand results
- Created a consistent pattern for formatting output across prompts
- Improved error handling in metadata extraction
- Standardized import organization and naming conventions
- Fixed various type checking issues across the codebase
This PR is part of our ongoing effort to improve the MCP's interaction
quality with LLMs, making the system more helpful and intuitive for AI
assistants to navigate knowledge bases.
🤖 Generated with [Claude Code](https://claude.ai/code)
---------
Co-authored-by: phernandez <phernandez@basicmachines.co>
- incremental sync on watch
- sync non-markdown files in knowledge base
- experimental `read_resource` tool for reading non-markdown files in raw form (pdf, image)
Paul Hernandez