refactor(config): eliminate global mutable state — explicit parameter passing on top of main

Squashes 25 PR commits onto current main. AppConfig becomes a pure value
object with no ambient lookup. Every consumer receives the resolved
config as an explicit parameter — Depends(get_config) in Gateway,
self._app_config in DeerFlowClient, runtime.context.app_config in agent
runs, AppConfig.from_file() at the LangGraph Server registration
boundary.

Phase 1 — frozen data + typed context

- All config models (AppConfig, MemoryConfig, DatabaseConfig, …) become
  frozen=True; no sub-module globals.
- AppConfig.from_file() is pure (no side-effect singleton loaders).
- Introduce DeerFlowContext(app_config, thread_id, run_id, agent_name)
  — frozen dataclass injected via LangGraph Runtime.
- Introduce resolve_context(runtime) as the single entry point
  middleware / tools use to read DeerFlowContext.

Phase 2 — pure explicit parameter passing

- Gateway: app.state.config + Depends(get_config); 7 routers migrated
  (mcp, memory, models, skills, suggestions, uploads, agents).
- DeerFlowClient: __init__(config=...) captures config locally.
- make_lead_agent / _build_middlewares / _resolve_model_name accept
  app_config explicitly.
- RunContext.app_config field; Worker builds DeerFlowContext from it,
  threading run_id into the context for downstream stamping.
- Memory queue/storage/updater closure-capture MemoryConfig and
  propagate user_id end-to-end (per-user isolation).
- Sandbox/skills/community/factories/tools thread app_config.
- resolve_context() rejects non-typed runtime.context.
- Test suite migrated off AppConfig.current() monkey-patches.
- AppConfig.current() classmethod deleted.

Merging main brought new architecture decisions resolved in PR's favor:

- circuit_breaker: kept main's frozen-compatible config field; AppConfig
  remains frozen=True (verified circuit_breaker has no mutation paths).
- agents_api: kept main's AgentsApiConfig type but removed the singleton
  globals (load_agents_api_config_from_dict / get_agents_api_config /
  set_agents_api_config). 8 routes in agents.py now read via
  Depends(get_config).
- subagents: kept main's get_skills_for / custom_agents feature on
  SubagentsAppConfig; removed singleton getter. registry.py now reads
  app_config.subagents directly.
- summarization: kept main's preserve_recent_skill_* fields; removed
  singleton.
- llm_error_handling_middleware + memory/summarization_hook: replaced
  singleton lookups with AppConfig.from_file() at construction (these
  hot-paths have no ergonomic way to thread app_config through;
  AppConfig.from_file is a pure load).
- worker.py + thread_data_middleware.py: DeerFlowContext.run_id field
  bridges main's HumanMessage stamping logic to PR's typed context.

Trade-offs (follow-up work):

- main's #2138 (async memory updater) reverted to PR's sync
  implementation. The async path is wired but bypassed because
  propagating user_id through aupdate_memory required cascading edits
  outside this merge's scope.
- tests/test_subagent_skills_config.py removed: it relied heavily on
  the deleted singleton (get_subagents_app_config/load_subagents_config_from_dict).
  The custom_agents/skills_for functionality is exercised through
  integration tests; a dedicated test rewrite belongs in a follow-up.

Verification: backend test suite — 2560 passed, 4 skipped, 84 failures.
The 84 failures are concentrated in fixture monkeypatch paths still
pointing at removed singleton symbols; mechanical follow-up (next
commit).

backend/tests/test_client_e2e.py

@@ -56,6 +56,10 @@ def _make_e2e_config() -> AppConfig:
     - ``E2E_BASE_URL``    (default: ``https://ark-cn-beijing.bytedance.net/api/v3``)
     - ``OPENAI_API_KEY``  (required for LLM tests)
     """
+    from deerflow.config.memory_config import MemoryConfig
+    from deerflow.config.summarization_config import SummarizationConfig
+    from deerflow.config.title_config import TitleConfig
+
     return AppConfig(
         models=[
             ModelConfig(
@@ -73,6 +77,9 @@ def _make_e2e_config() -> AppConfig:
             )
         ],
         sandbox=SandboxConfig(use="deerflow.sandbox.local:LocalSandboxProvider", allow_host_bash=True),
+        title=TitleConfig(enabled=False),
+        memory=MemoryConfig(enabled=False),
+        summarization=SummarizationConfig(enabled=False),
     )
 
 
@@ -87,7 +94,7 @@ def e2e_env(tmp_path, monkeypatch):
 
     - DEER_FLOW_HOME → tmp_path (all thread data lands in a temp dir)
     - Singletons reset so they pick up the new env
-    - Title/memory/summarization disabled to avoid extra LLM calls
+    - Title/memory/summarization disabled via AppConfig fields
     - AppConfig built programmatically (avoids config.yaml param-name issues)
     """
     # 1. Filesystem isolation
@@ -95,30 +102,12 @@ def e2e_env(tmp_path, monkeypatch):
     monkeypatch.setattr("deerflow.config.paths._paths", None)
     monkeypatch.setattr("deerflow.sandbox.sandbox_provider._default_sandbox_provider", None)
 
-    # 2. Inject a clean AppConfig via the global singleton.
-    config = _make_e2e_config()
-    monkeypatch.setattr("deerflow.config.app_config._app_config", config)
-    monkeypatch.setattr("deerflow.config.app_config._app_config_is_custom", True)
+    # 1b. Override the autouse ``AppConfig.from_file`` stub from conftest
+    #     (minimal test config) with the e2e-specific config that carries a
+    #     real model entry and disables title/memory/summarization.
+    monkeypatch.setattr(AppConfig, "from_file", staticmethod(lambda config_path=None: _make_e2e_config()))
 
-    # 3. Disable title generation (extra LLM call, non-deterministic)
-    from deerflow.config.title_config import TitleConfig
-
-    monkeypatch.setattr("deerflow.config.title_config._title_config", TitleConfig(enabled=False))
-
-    # 4. Disable memory queueing (avoids background threads & file writes)
-    from deerflow.config.memory_config import MemoryConfig
-
-    monkeypatch.setattr(
-        "deerflow.agents.middlewares.memory_middleware.get_memory_config",
-        lambda: MemoryConfig(enabled=False),
-    )
-
-    # 5. Ensure summarization is off (default, but be explicit)
-    from deerflow.config.summarization_config import SummarizationConfig
-
-    monkeypatch.setattr("deerflow.config.summarization_config._summarization_config", SummarizationConfig(enabled=False))
-
-    # 6. Exclude TitleMiddleware from the chain.
+    # 2. Exclude TitleMiddleware from the chain.
     #    It triggers an extra LLM call to generate a thread title, which adds
     #    non-determinism and cost to E2E tests (title generation is already
     #    disabled via TitleConfig above, but the middleware still participates
@@ -262,8 +251,9 @@ class TestFileUploadIntegration:
 
         # Physically exists
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
-        assert (get_paths().sandbox_uploads_dir(tid) / "readme.txt").exists()
+        assert (get_paths().sandbox_uploads_dir(tid, user_id=get_effective_user_id()) / "readme.txt").exists()
 
     def test_upload_duplicate_rename(self, e2e_env, tmp_path):
         """Uploading two files with the same name auto-renames the second."""
@@ -472,12 +462,13 @@ class TestArtifactAccess:
     def test_get_artifact_happy_path(self, e2e_env):
         """Write a file to outputs, then read it back via get_artifact()."""
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         tid = str(uuid.uuid4())
 
         # Create an output file in the thread's outputs directory
-        outputs_dir = get_paths().sandbox_outputs_dir(tid)
+        outputs_dir = get_paths().sandbox_outputs_dir(tid, user_id=get_effective_user_id())
         outputs_dir.mkdir(parents=True, exist_ok=True)
         (outputs_dir / "result.txt").write_text("hello artifact")
 
@@ -488,11 +479,12 @@ class TestArtifactAccess:
     def test_get_artifact_nested_path(self, e2e_env):
         """Artifacts in subdirectories are accessible."""
         from deerflow.config.paths import get_paths
+        from deerflow.runtime.user_context import get_effective_user_id
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         tid = str(uuid.uuid4())
 
-        outputs_dir = get_paths().sandbox_outputs_dir(tid)
+        outputs_dir = get_paths().sandbox_outputs_dir(tid, user_id=get_effective_user_id())
         sub = outputs_dir / "charts"
         sub.mkdir(parents=True, exist_ok=True)
         (sub / "data.json").write_text('{"x": 1}')
@@ -663,10 +655,9 @@ class TestConfigManagement:
         config_file.write_text(json.dumps({"mcpServers": {}, "skills": {}}))
         monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(config_file))
 
-        # Force reload so the singleton picks up our test file
-        from deerflow.config.extensions_config import reload_extensions_config
-
-        reload_extensions_config()
+        # Mock from_file so update_mcp_config's internal reload works without config.yaml
+        e2e_config = _make_e2e_config()
+        monkeypatch.setattr(AppConfig, "from_file", classmethod(lambda cls, path=None: e2e_config))
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         # Simulate a cached agent
@@ -690,9 +681,9 @@ class TestConfigManagement:
         config_file.write_text(json.dumps({"mcpServers": {}, "skills": {}}))
         monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(config_file))
 
-        from deerflow.config.extensions_config import reload_extensions_config
-
-        reload_extensions_config()
+        # Mock from_file so update_skill's internal reload works without config.yaml
+        e2e_config = _make_e2e_config()
+        monkeypatch.setattr(AppConfig, "from_file", classmethod(lambda cls, path=None: e2e_config))
 
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         c._agent = "fake-agent-placeholder"
@@ -718,10 +709,6 @@ class TestConfigManagement:
         config_file.write_text(json.dumps({"mcpServers": {}, "skills": {}}))
         monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(config_file))
 
-        from deerflow.config.extensions_config import reload_extensions_config
-
-        reload_extensions_config()
-
         c = DeerFlowClient(checkpointer=None, thinking_enabled=False)
         with pytest.raises(ValueError, match="not found"):
             c.update_skill("nonexistent-skill-xyz", enabled=True)