[Sebastiangmz]

Summary

• replace repository metadata persistence with a SQLite-backed RepositoryRegistry plus one-shot repositories.json migration
• add durable index/update/delete job rows and repository file/chunk metadata
• route API/MCP service state and UI repository state through the shared registry path
• extend deterministic EvalFly smoke checks and CI to include M2 coverage

Verification

• bun run /Users/sebastian/.omp/omp-pantheon/skills/specsafe/bin/specsafe.ts status -> OPEN before close; then SpecSafe end PASS
• PYTHONPATH=src .venv/bin/python -m pytest tests/test_m0_baseline.py tests/test_m1_services.py tests/test_m2_registry.py tests/test_api_routes.py tests/test_mcp_handlers.py tests/test_mcp_tools.py tests/test_ui_handlers.py -> 67 passed, 2 warnings
• .venv/bin/python -m ruff check src/coderag/services src/coderag/config.py src/coderag/api/routes.py src/coderag/mcp/handlers.py src/coderag/mcp/tools.py src/coderag/ui/repository_metadata.py src/coderag/ui/handlers.py tests/test_m1_services.py tests/test_m2_registry.py tests/test_api_routes.py tests/test_mcp_handlers.py tests/test_mcp_tools.py tests/test_ui_handlers.py scripts/evalfly_smoke.py -> OK
• PYTHONPATH=src .venv/bin/python -m mypy src/coderag/services src/coderag/config.py src/coderag/ui/repository_metadata.py src/coderag/ui/handlers.py tests/test_m1_services.py tests/test_m2_registry.py tests/test_api_routes.py tests/test_ui_handlers.py scripts/evalfly_smoke.py -> OK
• .venv/bin/python scripts/evalfly_smoke.py --suite smoke -> evalfly committed smoke passed: 13 cases
• .venv/bin/python -m py_compile src/coderag/services/*.py src/coderag/api/routes.py src/coderag/mcp/handlers.py src/coderag/ui/repository_metadata.py src/coderag/ui/handlers.py tests/test_m1_services.py tests/test_m2_registry.py tests/test_api_routes.py tests/test_ui_handlers.py -> success
• .venv/bin/python -m build -> Successfully built code_rag_me-0.1.2.tar.gz and code_rag_me-0.1.2-py3-none-any.whl

Scope guard

No hybrid retrieval, verified citation semantics, graph extraction, context pack APIs, or autonomous editing behavior added.

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