fix(db): close SQLite connections explicitly to suppress ResourceWarning on Python 3.13

`sqlite3.Connection.__exit__` only commits/rolls back a transaction — it
does not close the connection. Python 3.13 (the Nix env on the KVM
runner) emits `ResourceWarning: unclosed database` for every connection
GC'd without an explicit close, producing noisy output in the coverage job.

Add `DbStore._connection()`, a `contextmanager` that calls `self._connect()`,
wraps it in the existing transaction context manager, and closes the
connection in a `finally` block. Change all `with self._connect() as conn:`
call sites in `db_store.py`, `audit_store.py`, `queue_store.py`, and
`orchestrator/registry.py` to `with self._connection() as conn:`.
`_connect()` remains as the per-subclass hook (RegistryStore overrides
it to set `busy_timeout`); `_connection()` delegates to `self._connect()` so
the override is respected.

bot_bottle/db_store.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import sqlite3
+from contextlib import contextmanager
 from pathlib import Path
 
 try:
@@ -28,12 +29,21 @@ class DbStore:
         conn.row_factory = sqlite3.Row
         return conn
 
+    @contextmanager
+    def _connection(self):
+        conn = self._connect()
+        try:
+            with conn:
+                yield conn
+        finally:
+            conn.close()
+
     def is_migrated(self) -> bool:
         """Return True if the DB is fully up-to-date, False if migration is needed."""
         if not self.db_path.exists():
             return False
         try:
-            with self._connect() as conn:
+            with self._connection() as conn:
                 row = conn.execute(
                     "SELECT version FROM schema_versions WHERE module = ?",
                     (self._migrations.schema_key,),
@@ -45,7 +55,7 @@ class DbStore:
 
     def migrate(self) -> None:
         """Apply any pending migrations and set permissions on the DB file."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             self._migrations.apply(conn)
         self._chmod()