fix: #3346 clean up branch-only messages when deleting branches

src/agents/extensions/memory/advanced_sqlite_session.py

@@ -487,30 +487,22 @@ def _cleanup_sync():
 
     def _cleanup_orphaned_messages_sync(self, conn: sqlite3.Connection) -> int:
         with closing(conn.cursor()) as cursor:
-            # Find messages without structure metadata.
             cursor.execute(
                 f"""
-                SELECT am.id
-                FROM {self.messages_table} am
-                LEFT JOIN message_structure ms ON am.id = ms.message_id
-                WHERE am.session_id = ? AND ms.message_id IS NULL
-            """,
-                (self.session_id,),
-            )
-
-            orphaned_ids = [row[0] for row in cursor.fetchall()]
-
-            if not orphaned_ids:
-                return 0
-
-            placeholders = ",".join("?" * len(orphaned_ids))
-            cursor.execute(
-                f"DELETE FROM {self.messages_table} WHERE id IN ({placeholders})",
-                orphaned_ids,
+                DELETE FROM {self.messages_table}
+                WHERE session_id = ?
+                AND id NOT IN (
+                    SELECT message_id
+                    FROM message_structure ms
+                    WHERE ms.session_id = ?
+                )
+                """,
+                (self.session_id, self.session_id),
             )
 
             deleted_count = cursor.rowcount
-            self._logger.info(f"Cleaned up {deleted_count} orphaned messages")
+            if deleted_count:
+                self._logger.info(f"Cleaned up {deleted_count} orphaned messages")
             return deleted_count
 
     def _classify_message_type(self, item: TResponseInputItem) -> str:
@@ -786,14 +778,19 @@ def _delete_sync():
 
                     structure_deleted = cursor.rowcount
 
+                    orphaned_messages_deleted = self._cleanup_orphaned_messages_sync(conn)
+
                     conn.commit()
 
-                    return usage_deleted, structure_deleted
+                    return usage_deleted, structure_deleted, orphaned_messages_deleted
 
-        usage_deleted, structure_deleted = await asyncio.to_thread(_delete_sync)
+        usage_deleted, structure_deleted, orphaned_messages_deleted = await asyncio.to_thread(
+            _delete_sync
+        )
 
         self._logger.info(
-            f"Deleted branch '{branch_id}': {structure_deleted} message entries, {usage_deleted} usage entries"  # noqa: E501
+            f"Deleted branch '{branch_id}': {structure_deleted} message entries, "
+            f"{usage_deleted} usage entries, {orphaned_messages_deleted} orphaned messages"
         )
 
     async def list_branches(self) -> list[dict[str, Any]]:

tests/extensions/memory/test_advanced_sqlite_session.py

@@ -442,6 +442,168 @@ async def test_branching_functionality(agent: Agent):
     session.close()
 
 
+async def test_delete_branch_removes_branch_only_messages():
+    """Deleting a branch should not leave unreferenced branch-only messages behind."""
+    session_id = "branch_delete_cleanup_test"
+    session = AdvancedSQLiteSession(session_id=session_id, create_tables=True)
+
+    main_items: list[TResponseInputItem] = [
+        {"role": "user", "content": "First question"},
+        {"role": "assistant", "content": "First answer"},
+        {"role": "user", "content": "Second question"},
+        {"role": "assistant", "content": "Second answer"},
+    ]
+    await session.add_items(main_items)
+
+    await session.create_branch_from_turn(2, "cleanup_branch")
+    branch_items: list[TResponseInputItem] = [
+        {"role": "user", "content": "Branch-only question"},
+        {"role": "assistant", "content": "Branch-only answer"},
+    ]
+    await session.add_items(branch_items)
+
+    await session.delete_branch("cleanup_branch", force=True)
+
+    with session._locked_connection() as conn:
+        rows = conn.execute(
+            f"""
+            SELECT message_data
+            FROM {session.messages_table}
+            WHERE session_id = ?
+            ORDER BY id
+            """,
+            (session.session_id,),
+        ).fetchall()
+
+    contents = [json.loads(message_data)["content"] for (message_data,) in rows]
+    assert contents == [
+        "First question",
+        "First answer",
+        "Second question",
+        "Second answer",
+    ]
+    assert await session.get_items(branch_id="main") == main_items
+
+    session.close()
+
+
+async def test_delete_branch_keeps_messages_still_referenced_by_another_branch():
+    """Deleting one branch should keep messages inherited by a surviving branch."""
+    session = AdvancedSQLiteSession(
+        session_id="branch_delete_shared_descendant_test",
+        create_tables=True,
+    )
+
+    main_items: list[TResponseInputItem] = [
+        {"role": "user", "content": "Main first question"},
+        {"role": "assistant", "content": "Main first answer"},
+        {"role": "user", "content": "Main second question"},
+        {"role": "assistant", "content": "Main second answer"},
+    ]
+    branch_a_shared_items: list[TResponseInputItem] = [
+        {"role": "user", "content": "Branch A shared question"},
+        {"role": "assistant", "content": "Branch A shared answer"},
+    ]
+    branch_a_only_items: list[TResponseInputItem] = [
+        {"role": "user", "content": "Branch A only question"},
+        {"role": "assistant", "content": "Branch A only answer"},
+    ]
+
+    try:
+        await session.add_items(main_items)
+        await session.create_branch_from_turn(2, "branch_a")
+        await session.add_items(branch_a_shared_items + branch_a_only_items)
+
+        await session.create_branch_from_turn(3, "branch_b")
+        await session.delete_branch("branch_a")
+
+        with session._locked_connection() as conn:
+            rows = conn.execute(
+                f"""
+                SELECT message_data
+                FROM {session.messages_table}
+                WHERE session_id = ?
+                ORDER BY id
+                """,
+                (session.session_id,),
+            ).fetchall()
+
+        contents = [json.loads(message_data)["content"] for (message_data,) in rows]
+        assert "Branch A shared question" in contents
+        assert "Branch A shared answer" in contents
+        assert "Branch A only question" not in contents
+        assert "Branch A only answer" not in contents
+        assert await session.get_items(branch_id="branch_b") == [
+            *main_items[:2],
+            *branch_a_shared_items,
+        ]
+    finally:
+        session.close()
+
+
+async def test_orphan_cleanup_uses_set_based_delete_for_many_messages():
+    """Orphan cleanup should not build one DELETE parameter per orphaned row."""
+
+    class RecordingCursor:
+        def __init__(self, cursor: Any, connection: "RecordingConnection") -> None:
+            self._cursor = cursor
+            self._connection = connection
+
+        @property
+        def rowcount(self) -> int:
+            return cast(int, self._cursor.rowcount)
+
+        def execute(self, sql: str, parameters: Any = None) -> Any:
+            normalized_sql = " ".join(sql.split()).upper()
+            if normalized_sql.startswith("DELETE"):
+                self._connection.delete_parameter_counts.append(len(parameters or ()))
+            if parameters is None:
+                return self._cursor.execute(sql)
+            return self._cursor.execute(sql, parameters)
+
+        def fetchall(self) -> Any:
+            return self._cursor.fetchall()
+
+        def close(self) -> None:
+            self._cursor.close()
+
+    class RecordingConnection:
+        def __init__(self, conn: Any) -> None:
+            self._conn = conn
+            self.delete_parameter_counts: list[int] = []
+
+        def cursor(self) -> RecordingCursor:
+            return RecordingCursor(self._conn.cursor(), self)
+
+    session = AdvancedSQLiteSession(
+        session_id="branch_delete_many_orphans_cleanup",
+        create_tables=True,
+    )
+    orphan_items: list[TResponseInputItem] = [
+        {"role": "user", "content": f"orphan {i}"} for i in range(1200)
+    ]
+
+    try:
+        with session._locked_connection() as conn:
+            session._insert_items(conn, orphan_items)
+            conn.commit()
+
+            recording_conn = RecordingConnection(conn)
+            deleted_count = session._cleanup_orphaned_messages_sync(cast(Any, recording_conn))
+            conn.commit()
+
+            remaining_count = conn.execute(
+                f"SELECT COUNT(*) FROM {session.messages_table} WHERE session_id = ?",
+                (session.session_id,),
+            ).fetchone()[0]
+
+        assert deleted_count == len(orphan_items)
+        assert remaining_count == 0
+        assert recording_conn.delete_parameter_counts == [2]
+    finally:
+        session.close()
+
+
 async def test_get_conversation_turns():
     """Test get_conversation_turns functionality."""
     session_id = "conversation_turns_test"