## Problem
`headroom memory delete`, `prune`, `edit`, and `purge` all operate on
the bare `SQLiteMemoryStore` — they update the primary `memories` table
but never touch the FTS5 full-text index (`memory_fts` in `memory.db`)
or the vector index (`vec_metadata` / `vec_embeddings` in
`memory_vectors.db`). The index maintenance path lives in
`HierarchicalMemory.delete()` / `.update()`, which the CLI never
instantiates.
**Symptoms (from #2856):**
```sql
-- After deleting 16 of 46 memories via CLI:
SELECT COUNT(*) FROM memories; -- 30
SELECT COUNT(*) FROM memory_fts; -- 46 ← orphans
-- memory_vectors.db
SELECT COUNT(*) FROM vec_metadata; -- 46 ← orphans
```
Deleted memories keep surfacing in `memory_search` results even after a
full server restart, because server startup only re-embeds memories
whose `embedding IS NULL` — it never removes orphaned index entries.
Fixes#2856.
## Solution
Add two best-effort helpers to `headroom/cli/memory.py` that use
**direct SQLite** (no `sqlite-vec` extension, no embedder):
- **`_remove_from_search_indexes(db_path, memory_ids)`**: removes
specific IDs from `memory_fts` and from `vec_metadata` /
`vec_embeddings`. Skips silently if an index doesn't exist.
- **`_clear_all_search_indexes(db_path)`**: truncates both indexes
completely (for purge).
Wire these up in four commands:
| Command | Change |
|---|---|
| `delete` | `_remove_from_search_indexes` after `store.delete_batch()`
|
| `prune` | `_remove_from_search_indexes` after `store.delete_batch()` |
| `purge` | `_clear_all_search_indexes` after `store.clear_all()` |
| `edit` | If content changed: remove stale entries, clear `embedding`
(server re-embeds on next startup), re-add FTS5 entry with new content
immediately |
The edit path re-adds the FTS5 entry right away so keyword search
reflects the new content without requiring a server restart. Vector
search is deferred to the next startup re-embed cycle (same as what the
server already does for missing embeddings).
## Changes
- `headroom/cli/memory.py` — two new helpers; four command call sites
- `tests/test_cli_memory_index_sync.py` (new) — 9 unit tests covering
both helpers with FTS5 and a stub vector DB. No `sqlite-vec` or embedder
required; tests run locally.
## Testing
```
$ python -m pytest tests/test_cli_memory_index_sync.py -v
...
9 passed in 2.38s
```
---------
Signed-off-by: Radhakrishnan Pachyappan <radhakrishnan.p@op.tech>
Signed-off-by: Radhakrishnan Pachyappan <gingeekrishna@gmail.com>
Co-authored-by: Tejas Chopra <tejas@Tejass-MacBook-Pro.local>
