refactor(store): consolidate the SQLite store family into bot_bottle.store

Move the DbStore base (db_store), the shared schema-migration base (migrations /
TableMigrations), the concrete stores (audit_store, config_store, queue_store),
and StoreManager out of the package root into a bot_bottle/store/ package, so
persistence lives in one place rather than scattered across the root.

Callers use direct submodule imports (from bot_bottle.store.store_manager
import StoreManager). Inside the moved modules the relative imports point back
up to their non-store siblings (..paths, ..supervise_types) while co-moved
siblings stay package-local; the flat-import fallbacks are untouched. The
orchestrator's own stores (config_store, secret_store, registry) stay in
orchestrator/ and repoint to the moved DbStore / TableMigrations.

No behavior change; full unit suite green.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

bot_bottle/store/db_store.py

@@ -0,0 +1,69 @@
+"""Shared SQLite-backed store base class for bot-bottle (PRD 0013)."""
+
+from __future__ import annotations
+
+import sqlite3
+from contextlib import contextmanager
+from pathlib import Path
+
+try:
+    from .migrations import TableMigrations
+except ImportError:
+    from migrations import TableMigrations  # type: ignore[import-not-found]  # pylint: disable=import-error,no-name-in-module
+
+
+class DbVersionError(Exception):
+    """Raised when the on-disk schema is behind the current migration list."""
+
+
+class DbStore:
+    """Base for SQLite-backed stores. Subclasses resolve db_path then call super().__init__."""
+
+    def __init__(self, db_path: Path, migrations: TableMigrations) -> None:
+        self.db_path = db_path
+        self._migrations = migrations
+        self.db_path.parent.mkdir(parents=True, exist_ok=True)
+
+    def _connect(self) -> sqlite3.Connection:
+        conn = sqlite3.connect(self.db_path)
+        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._connection() as conn:
+                row = conn.execute(
+                    "SELECT version FROM schema_versions WHERE module = ?",
+                    (self._migrations.schema_key,),
+                ).fetchone()
+        except sqlite3.OperationalError:
+            return False
+        version = row[0] if row else 0
+        return version == len(self._migrations.migrations)
+
+    def migrate(self) -> None:
+        """Apply any pending migrations and set permissions on the DB file."""
+        with self._connection() as conn:
+            self._migrations.apply(conn)
+        self._chmod()
+
+    def _chmod(self) -> None:
+        try:
+            self.db_path.chmod(0o600)
+        except OSError:
+            pass
+
+
+__all__ = ["DbStore", "DbVersionError"]