Phase 2 of cleanup now sweeps _index.json for stale entries with no
backing file and no in-memory session, removing them regardless of
title (catches multi-language 'Untitled' variants). Phase 3 only
deletes the index when Phase 1 removed files AND Phase 2 couldn't
run, fixing the cache-busting on every cleanup call.
Fix two phase-interaction bugs flagged by Greptile review:
- Track phase1_removed_ids to prevent Phase 2 double-counting
sessions already removed from disk by Phase 1.
- Track phase2_rewrote_index so Phase 3 skips deletion when
Phase 2 already cleaned the index in-place.
Adds test_issue5331_index_only_ghost_cleanup.py with 12 test cases.
