Why

On macOS, MCP startup failed during migration 0042 with OperationalError: no such module: vec0. The path migration reflected every table, including an existing search_vector_embeddings virtual table, on a connection without sqlite-vec loaded.

What Changed

Restrict column reflection to tables referenced by the migration's twin cleanup and path normalization statements.

Implementation Details

The migration already intentionally leaves embeddings to the orphan sweeper. Restricting reflection preserves that behavior without making path normalization depend on the optional vector extension. This repairs the existing migration so databases blocked before 0042 can upgrade.

Testing

• Added a real sqlite-vec table with an embedding, then upgraded through a separate extension-free Alembic connection. The test reproduced the exact startup exception before the fix and passes afterward, verifying twin merging, accepted content preservation, and unchanged embeddings.
• BASIC_MEMORY_ENV=test LOGFIRE_IGNORE_NO_CONFIG=1 uv run pytest -q tests/test_nfc_file_paths_migration.py tests/test_alembic_env.py tests/test_migration_graph.py --no-cov: 31 passed.
• just fast-check: lint and typecheck passed; unrelated formatting was reverted.
• just doctor: passed.
• User confirmed the MCP connection works after restarting with the fix.

Risks / Follow-ups

No new migration or vector-table mutations. Databases that already applied 0042 do not rerun it.