Merge pull request #5 from Phasm22/cursor/reliability-refactor-mcp-first

Enhance configuration and retrieval features

Align doc_type taxonomy with list_silos; fix explain_retrieval metrics; add pal extension pack and MCP stale warning.

feat: ingest orchestration (run_ingest) and MCP/CLI convergence

Merge pull request #4 from Phasm22/cursor/reliability-refactor-mcp-first

refactor: split query orchestration, ingest package, pal registry; chroma locks + DI hooks

MCP Chroma serialization, DB storage diagnostics, ingest/processor fixes

Fix ChromaDB SIGSEGV on macOS ARM64: upgrade to 1.5.5, drop clear_system_cache()

Merge pull request #3 from Phasm22/cursor/reliability-refactor-mcp-first

Reliability refactor: single ChromaDB client, atomic ingest, MCP-first ops, macOS hardware optimizations

Implement orphaned source detection and enhance error reporting in silo audit

Enhance CLI and MCP server functionality with improved indexing and retrieval features

Update .gitignore, enhance CLAUDE.md, and improve mcp_server.py functionality

Implement silo repair command and enhance retrieval functions

Enhance database path resolution and improve retrieval functions