Remove the early return in update_same_commit that skipped filesystem validation when git reported no changes. Add prune_stale_entries to finalize_and_cache so every vault scan path validates entries exist on disk and deduplicates by case-folded path. Prevents ghost notes after deleting files outside the app (e.g., via Finder). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>