Clean up orphaned messages when deleting a branch

src/agents/extensions/memory/advanced_sqlite_session.py

@@ -786,14 +786,18 @@ def _delete_sync():
 
                     structure_deleted = cursor.rowcount
 
+                    # Remove messages that are no longer referenced by any branch.
+                    orphans_deleted = self._cleanup_orphaned_messages_sync(conn)
+
                     conn.commit()
 
-                    return usage_deleted, structure_deleted
+                    return usage_deleted, structure_deleted, orphans_deleted
 
-        usage_deleted, structure_deleted = await asyncio.to_thread(_delete_sync)
+        usage_deleted, structure_deleted, orphans_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, {orphans_deleted} orphaned messages"
         )
 
     async def list_branches(self) -> list[dict[str, Any]]:

tests/extensions/memory/test_advanced_sqlite_session.py

@@ -694,6 +694,49 @@ async def test_branch_deletion_with_force():
     session.close()
 
 
+async def test_delete_branch_removes_orphaned_messages():
+    """Regression: delete_branch must remove messages exclusive to that branch.
+
+    Messages shared with another branch must be kept; messages that exist only
+    in the deleted branch must be cleaned up from the messages table.
+    """
+    session = AdvancedSQLiteSession(session_id="orphan_delete_test", create_tables=True)
+
+    # Two messages on main branch.
+    await session.add_items([{"role": "user", "content": "main msg 1"}])
+    await session.add_items([{"role": "user", "content": "main msg 2"}])
+
+    # Branch from turn 1; this branch shares main msg 1 and adds its own message.
+    await session.create_branch_from_turn(1, "side_branch")
+    await session.add_items([{"role": "user", "content": "branch only msg"}])
+
+    # Confirm all three messages are in the messages table before deletion.
+    with session._locked_connection() as conn:
+        total_before = conn.execute(
+            f"SELECT COUNT(*) FROM {session.messages_table} WHERE session_id = ?",
+            (session.session_id,),
+        ).fetchone()[0]
+    assert total_before == 3
+
+    await session.switch_to_branch("main")
+    await session.delete_branch("side_branch")
+
+    # The branch-only message must be gone; the shared message must remain.
+    with session._locked_connection() as conn:
+        total_after = conn.execute(
+            f"SELECT COUNT(*) FROM {session.messages_table} WHERE session_id = ?",
+            (session.session_id,),
+        ).fetchone()[0]
+    assert total_after == 2, "branch-only messages must be deleted when the branch is removed"
+
+    # Main branch items must still be intact.
+    await session.switch_to_branch("main")
+    main_items = await session.get_items()
+    assert len(main_items) == 2
+
+    session.close()
+
+
 async def test_get_items_with_parameters():
     """Test get_items with new parameters (include_inactive, branch_id)."""
     session_id = "get_items_params_test"