Maintenance

bookmark-context vacuum

Stop the daemon first — two processes must not open the Chroma store at once.

vacuum removes data the SQLite and Chroma stores no longer agree on:

• rows orphaned while SQLite foreign keys were off,
• Chroma collections whose SQLite collection is gone,
• vectors no chunk row points at any more — the surplus a re-index leaves when a page yields fewer chunks than before.

It also resets bookmarks stuck in indexing by a daemon that stopped, so they show as retryable errors instead of hanging in progress. It prints a count per category.

Safe to run repeatedly; a second pass on clean data deletes nothing.