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/queue_store.py

@@ -0,0 +1,234 @@
+"""SQLite-backed queue store for supervise proposals and responses (PRD 0013)."""
+
+from __future__ import annotations
+
+import os
+import sqlite3
+from pathlib import Path
+
+try:
+    from ..supervise_types import Proposal, Response
+    from ..paths import host_db_path
+    from .db_store import DbStore
+    from .migrations import TableMigrations
+except ImportError:
+    from supervise_types import Proposal, Response  # 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 QueueStore(DbStore):
+    """SQLite-backed persistent store for supervise proposals and responses."""
+
+    def __init__(self, queue_key: str, db_path: Path | None = None) -> None:
+        self.queue_key = queue_key
+        if db_path is not None:
+            resolved = db_path
+        else:
+            # In the gateway container SUPERVISE_DB_PATH points at the
+            # bind-mounted host DB. On the host this env var is never set,
+            # so we always fall through to host_db_path().
+            env_path = os.environ.get("SUPERVISE_DB_PATH", "").strip()
+            resolved = Path(env_path) if env_path else host_db_path()
+        # 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("queue_store", [
+            # v1 — proposals table
+            """
+            CREATE TABLE IF NOT EXISTS supervise_proposals (
+                queue_key TEXT NOT NULL,
+                id TEXT NOT NULL,
+                bottle_slug TEXT NOT NULL,
+                tool TEXT NOT NULL,
+                proposed_file TEXT NOT NULL,
+                justification TEXT NOT NULL,
+                arrival_timestamp TEXT NOT NULL,
+                current_file_hash TEXT NOT NULL,
+                archived INTEGER NOT NULL DEFAULT 0,
+                PRIMARY KEY (queue_key, id)
+            )
+            """,
+            # v2 — responses table
+            """
+            CREATE TABLE IF NOT EXISTS supervise_responses (
+                queue_key TEXT NOT NULL,
+                proposal_id TEXT NOT NULL,
+                status TEXT NOT NULL,
+                notes TEXT NOT NULL,
+                final_file TEXT,
+                archived INTEGER NOT NULL DEFAULT 0,
+                PRIMARY KEY (queue_key, proposal_id)
+            )
+            """,
+        ])
+        super().__init__(resolved, migrations)
+
+    def write_proposal(self, proposal: Proposal) -> Path:
+        with self._connection() as conn:
+            conn.execute(
+                """
+                INSERT OR REPLACE INTO supervise_proposals (
+                    queue_key, id, bottle_slug, tool, proposed_file, justification,
+                    arrival_timestamp, current_file_hash, archived
+                ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, 0)
+                """,
+                (
+                    self.queue_key,
+                    proposal.id,
+                    proposal.bottle_slug,
+                    proposal.tool,
+                    proposal.proposed_file,
+                    proposal.justification,
+                    proposal.arrival_timestamp,
+                    proposal.current_file_hash,
+                ),
+            )
+        self._chmod()
+        return self.db_path
+
+    def read_proposal(self, proposal_id: str) -> Proposal:
+        with self._connection() as conn:
+            row = conn.execute(
+                """
+                SELECT * FROM supervise_proposals
+                WHERE queue_key = ? AND id = ? AND archived = 0
+                """,
+                (self.queue_key, proposal_id),
+            ).fetchone()
+        if row is None:
+            raise FileNotFoundError(proposal_id)
+        return self._row_to_proposal(row)
+
+    def list_pending_proposals(self) -> list[Proposal]:
+        if not self.db_path.is_file():
+            return []
+        with self._connection() as conn:
+            rows = conn.execute(
+                """
+                SELECT p.* FROM supervise_proposals p
+                WHERE p.archived = 0
+                  AND p.queue_key = ?
+                  AND NOT EXISTS (
+                    SELECT 1 FROM supervise_responses r
+                    WHERE r.queue_key = p.queue_key
+                      AND r.proposal_id = p.id
+                      AND r.archived = 0
+                  )
+                ORDER BY p.arrival_timestamp, p.id
+                """,
+                (self.queue_key,),
+            ).fetchall()
+        return [self._row_to_proposal(row) for row in rows]
+
+    def list_all_pending_proposals(self) -> list[Proposal]:
+        if not self.db_path.is_file():
+            return []
+        with self._connection() as conn:
+            rows = conn.execute(
+                """
+                SELECT p.* FROM supervise_proposals p
+                WHERE p.archived = 0
+                  AND NOT EXISTS (
+                    SELECT 1 FROM supervise_responses r
+                    WHERE r.queue_key = p.queue_key
+                      AND r.proposal_id = p.id
+                      AND r.archived = 0
+                  )
+                ORDER BY p.arrival_timestamp, p.id
+                """
+            ).fetchall()
+        return [self._row_to_proposal(row) for row in rows]
+
+    def write_response(self, response: Response) -> Path:
+        with self._connection() as conn:
+            conn.execute(
+                """
+                INSERT OR REPLACE INTO supervise_responses (
+                    queue_key, proposal_id, status, notes, final_file, archived
+                ) VALUES (?, ?, ?, ?, ?, 0)
+                """,
+                (
+                    self.queue_key,
+                    response.proposal_id,
+                    response.status,
+                    response.notes,
+                    response.final_file,
+                ),
+            )
+        self._chmod()
+        return self.db_path
+
+    def read_response(self, proposal_id: str) -> Response:
+        with self._connection() as conn:
+            row = conn.execute(
+                """
+                SELECT * FROM supervise_responses
+                WHERE queue_key = ? AND proposal_id = ? AND archived = 0
+                """,
+                (self.queue_key, proposal_id),
+            ).fetchone()
+        if row is None:
+            raise FileNotFoundError(proposal_id)
+        return self._row_to_response(row)
+
+    def archive_proposal(self, proposal_id: str) -> None:
+        if not self.db_path.is_file():
+            return
+        with self._connection() as conn:
+            conn.execute(
+                """
+                UPDATE supervise_proposals SET archived = 1
+                WHERE queue_key = ? AND id = ?
+                """,
+                (self.queue_key, proposal_id),
+            )
+            conn.execute(
+                """
+                UPDATE supervise_responses SET archived = 1
+                WHERE queue_key = ? AND proposal_id = ?
+                """,
+                (self.queue_key, proposal_id),
+            )
+
+    def archive_all(self) -> None:
+        """Archive every proposal + response for this queue key. Used to reap a
+        bottle's supervise records when it is torn down or reconciled away —
+        the retention path for a client that received a decision but died before
+        acknowledging it. Idempotent."""
+        if not self.db_path.is_file():
+            return
+        with self._connection() as conn:
+            conn.execute(
+                "UPDATE supervise_proposals SET archived = 1 WHERE queue_key = ?",
+                (self.queue_key,),
+            )
+            conn.execute(
+                "UPDATE supervise_responses SET archived = 1 WHERE queue_key = ?",
+                (self.queue_key,),
+            )
+
+    @staticmethod
+    def _row_to_proposal(row: sqlite3.Row) -> Proposal:
+        return Proposal(
+            id=row["id"],
+            bottle_slug=row["bottle_slug"],
+            tool=row["tool"],
+            proposed_file=row["proposed_file"],
+            justification=row["justification"],
+            arrival_timestamp=row["arrival_timestamp"],
+            current_file_hash=row["current_file_hash"],
+        )
+
+    @staticmethod
+    def _row_to_response(row: sqlite3.Row) -> Response:
+        return Response(
+            proposal_id=row["proposal_id"],
+            status=row["status"],
+            notes=row["notes"],
+            final_file=row["final_file"],
+        )
+
+
+__all__ = ["QueueStore"]