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/audit_store.py

@@ -0,0 +1,93 @@
+"""SQLite-backed audit store for supervise (PRD 0013)."""
+
+from __future__ import annotations
+
+import sqlite3
+from pathlib import Path
+
+try:
+    from ..supervise_types import AuditEntry
+    from ..paths import host_db_path
+    from .db_store import DbStore
+    from .migrations import TableMigrations
+except ImportError:
+    from supervise_types import AuditEntry  # type: ignore[import-not-found]  # pylint: disable=import-error,no-name-in-module
+    from paths import host_db_path  # type: ignore[import-not-found]  # pylint: disable=import-error,no-name-in-module
+    from db_store import DbStore  # type: ignore[import-not-found]  # pylint: disable=import-error,no-name-in-module
+    from migrations import TableMigrations  # type: ignore[import-not-found]  # pylint: disable=import-error,no-name-in-module
+
+
+class AuditStore(DbStore):
+    """SQLite-backed persistent store for supervise audit entries."""
+
+    def __init__(self, db_path: Path | None = None) -> None:
+        # One entry per schema version: migrations[0] brings a fresh DB to
+        # version 1, [1] to version 2, etc.  Add new entries at the end; never
+        # edit existing ones.
+        migrations = TableMigrations("audit_store", [
+            # v1 — initial schema
+            """
+            CREATE TABLE IF NOT EXISTS supervise_audit_entries (
+                id INTEGER PRIMARY KEY AUTOINCREMENT,
+                timestamp TEXT NOT NULL,
+                bottle_slug TEXT NOT NULL,
+                component TEXT NOT NULL,
+                operator_action TEXT NOT NULL,
+                operator_notes TEXT NOT NULL,
+                justification TEXT NOT NULL,
+                diff TEXT NOT NULL
+            )
+            """,
+        ])
+        super().__init__(db_path or host_db_path(), migrations)
+
+    def write_audit_entry(self, entry: AuditEntry) -> Path:
+        with self._connection() as conn:
+            conn.execute(
+                """
+                INSERT INTO supervise_audit_entries (
+                    timestamp, bottle_slug, component, operator_action,
+                    operator_notes, justification, diff
+                ) VALUES (?, ?, ?, ?, ?, ?, ?)
+                """,
+                (
+                    entry.timestamp,
+                    entry.bottle_slug,
+                    entry.component,
+                    entry.operator_action,
+                    entry.operator_notes,
+                    entry.justification,
+                    entry.diff,
+                ),
+            )
+        self._chmod()
+        return self.db_path
+
+    def read_audit_entries(self, component: str, slug: str) -> list[AuditEntry]:
+        if not self.db_path.is_file():
+            return []
+        with self._connection() as conn:
+            rows = conn.execute(
+                """
+                SELECT * FROM supervise_audit_entries
+                WHERE component = ? AND bottle_slug = ?
+                ORDER BY id
+                """,
+                (component, slug),
+            ).fetchall()
+        return [self._row_to_entry(row) for row in rows]
+
+    @staticmethod
+    def _row_to_entry(row: sqlite3.Row) -> AuditEntry:
+        return AuditEntry(
+            timestamp=row["timestamp"],
+            bottle_slug=row["bottle_slug"],
+            component=row["component"],
+            operator_action=row["operator_action"],
+            operator_notes=row["operator_notes"],
+            justification=row["justification"],
+            diff=row["diff"],
+        )
+
+
+__all__ = ["AuditStore"]