Move workspace roots onto thread/session state and stop using active permission profile modifications as an overlay for writable roots. Existing app-server threads now preserve their persisted PermissionProfile value across resume, fork, and turn updates; permissions requests on existing threads only update the active named profile after validating it exists. Workspace roots can be updated independently, and SandboxPolicy::WorkspaceWrite no longer stores its own writable_roots.

sdk/python/tests/test_client_rpc_methods.py

@@ -66,6 +66,7 @@ def test_thread_resume_response_accepts_auto_review_reviewer() -> None:
                 "id": "thread-1",
                 "modelProvider": "openai",
                 "preview": "",
+                "sessionId": "session-1",
                 "source": "cli",
                 "status": {"type": "idle"},
                 "turns": [],