Without this, every `second-brain process` run prints
couldn't stop thread 'pool-1-worker-N' within 5.0 seconds
during interpreter shutdown — psycopg_pool's background workers don't
get a clean stop signal before Python's threading shutdown deadline.
Registering close_pool via atexit the first time we open the pool fixes
it without changing any API. `close_pool` is already idempotent, so the
explicit teardown path in the smoke test (which calls it directly) and
the atexit path coexist safely.
Swap the SQLite backing store for petalbrain Postgres + pgvector, modeled
on vault-mcp. All second-brain relational tables now live in the
`second_brain` schema (owned by the lovebug role); embeddings are written
to the shared public.embeddings table.
Locked design decisions (per Travis):
- DB: existing petalbrain Postgres, second_brain schema, lovebug role.
- Connection: containerized homelab-postgres:5432, plain psycopg_pool
(min=1/max=10), no PgBouncer.
- ORM stays SQLAlchemy; int autoincrement PKs + naive UTC DateTime.
- Embeddings: reuse shared public.embeddings keyed by
(source_schema='second_brain', source_table='extractions', source_id,
model='nomic-embed-text'). Summaries only for this round.
- Pipeline: chunk_text → Ollama nomic-embed-text → delete-before-insert
upsert, with graceful degradation (no DB / no Ollama → log + skip).
- Alembic stands up second-brain's own schema; public.embeddings stays
out-of-band.
- File-based wiki compiler is unchanged.
No SQLite data import — starting clean.
This commit is the scaffolding only; `alembic upgrade head` and a smoke
test of the embedding path are the next checkpoint.
