Files deleted from disk (rm a.md) were leaving stale documents + chunks +
embeddings in the store, surfacing as ghost citations in search/ask.
Existing purge_orphan_at_workspace_path only handled content-changed
stale (WHERE workspace_path=? AND asset_id != ?) — file deletion has no
new asset_id.
Fix: post-walker-scan sweep. Compute (stored_paths - scanned_paths),
for each candidate check filesystem existence — only purge when the
file is TRULY missing. Scope-narrowing case (file on disk but outside
include glob) is explicitly NOT purged to protect users from accidental
data loss via config edits.
Adds:
- DocumentStore::all_workspace_paths trait method + SqliteStore impl
- purge_deleted_workspace_path in store-sqlite (returns chunk_ids for
vector delete; deletes doc CASCADE + asset row + copied storage file)
- sweep_deleted_files in kebab-app::ingest path; called once per ingest
before the per-asset loop
- IngestReport.purged_deleted_files counter (additive, serde default)
- CLI ingest summary mentions purge count when > 0
- 2 integration tests: file_deletion_auto_purge + include_scope_narrowing_does_NOT_purge
dogfood discovery (PR #142 1B + multi-root: kebab-docs + httpx + zod
+ lodash). Per user decision: only filesystem deletion auto-purges;
scope narrowing requires explicit kebab reset.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
