fix: keep new agent bootstrap in user scope (#2784)

backend/app/gateway/services.py

@@ -136,6 +136,24 @@ def merge_run_context_overrides(config: dict[str, Any], context: Mapping[str, An
                 runtime_context.setdefault(key, context[key])
 
 
+def inject_authenticated_user_context(config: dict[str, Any], request: Request) -> None:
+    """Stamp the authenticated user into the run context for background tools.
+
+    Tool execution may happen after the request handler has returned, so tools
+    that persist user-scoped files should not rely only on ambient ContextVars.
+    The value comes from server-side auth state, never from client context.
+    """
+
+    user = getattr(request.state, "user", None)
+    user_id = getattr(user, "id", None)
+    if user_id is None:
+        return
+
+    runtime_context = config.setdefault("context", {})
+    if isinstance(runtime_context, dict):
+        runtime_context["user_id"] = str(user_id)
+
+
 def resolve_agent_factory(assistant_id: str | None):
     """Resolve the agent factory callable from config.
 
@@ -288,6 +306,7 @@ async def start_run(
     # that carries agent configuration (model_name, thinking_enabled, etc.).
     # Only agent-relevant keys are forwarded; unknown keys (e.g. thread_id) are ignored.
     merge_run_context_overrides(config, getattr(body, "context", None))
+    inject_authenticated_user_context(config, request)
 
     stream_modes = normalize_stream_modes(body.stream_mode)
 

backend/packages/harness/deerflow/tools/builtins/setup_agent_tool.py

@@ -13,6 +13,13 @@ from deerflow.tools.types import Runtime
 logger = logging.getLogger(__name__)
 
 
+def _get_runtime_user_id(runtime: Runtime) -> str:
+    context_user_id = runtime.context.get("user_id") if runtime.context else None
+    if context_user_id:
+        return str(context_user_id)
+    return get_effective_user_id()
+
+
 @tool
 def setup_agent(
     soul: str,
@@ -38,7 +45,7 @@ def setup_agent(
         if agent_name:
             # Custom agents are persisted under the current user's bucket so
             # different users do not see each other's agents.
-            user_id = get_effective_user_id()
+            user_id = _get_runtime_user_id(runtime)
             agent_dir = paths.user_agent_dir(user_id, agent_name)
         else:
             # Default agent (no agent_name): SOUL.md lives at the global base dir.

backend/tests/test_gateway_services.py

@@ -324,6 +324,21 @@ def test_context_does_not_override_existing_configurable():
     assert config["configurable"]["subagent_enabled"] is True
 
 
+def test_inject_authenticated_user_context_overrides_client_user_id():
+    """Run context should carry the authenticated user, not client-supplied user_id."""
+    from types import SimpleNamespace
+
+    from app.gateway.services import build_run_config, inject_authenticated_user_context
+
+    config = build_run_config("thread-1", None, None)
+    config["context"] = {"user_id": "spoofed-client"}
+    request = SimpleNamespace(state=SimpleNamespace(user=SimpleNamespace(id="auth-user-42")))
+
+    inject_authenticated_user_context(config, request)
+
+    assert config["context"]["user_id"] == "auth-user-42"
+
+
 # ---------------------------------------------------------------------------
 # build_run_config — context / configurable precedence (LangGraph >= 0.6.0)
 # ---------------------------------------------------------------------------

backend/tests/test_setup_agent_tool.py

@@ -6,6 +6,8 @@ from pathlib import Path
 from types import SimpleNamespace
 from unittest.mock import MagicMock, patch
 
+import pytest
+
 from deerflow.tools.builtins.setup_agent_tool import setup_agent
 
 # --- Helpers ---
@@ -126,3 +128,23 @@ class TestSetupAgentNoDataLoss:
         assert agent_dir.exists()
         assert (agent_dir / "SOUL.md").read_text() == "# My Agent"
         assert (agent_dir / "config.yaml").exists()
+
+    @pytest.mark.no_auto_user
+    def test_runtime_user_id_used_when_contextvar_missing(self, tmp_path: Path):
+        """setup_agent should not fall back to default when runtime carries user_id."""
+        runtime = _DummyRuntime(
+            context={"agent_name": "test-agent", "user_id": "auth-user-42"},
+            tool_call_id="tool-3",
+        )
+
+        with patch("deerflow.tools.builtins.setup_agent_tool.get_paths", return_value=_make_paths_mock(tmp_path)):
+            setup_agent.func(
+                soul="# My Agent",
+                description="A test agent",
+                runtime=runtime,
+            )
+
+        expected_dir = tmp_path / "users" / "auth-user-42" / "agents" / "test-agent"
+        default_dir = tmp_path / "users" / "default" / "agents" / "test-agent"
+        assert (expected_dir / "SOUL.md").read_text() == "# My Agent"
+        assert not default_dir.exists()