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_memory_router.py

@@ -4,6 +4,18 @@ from fastapi import FastAPI
 from fastapi.testclient import TestClient
 
 from app.gateway.routers import memory
+from deerflow.config.app_config import AppConfig
+from deerflow.config.sandbox_config import SandboxConfig
+
+_TEST_APP_CONFIG = AppConfig(sandbox=SandboxConfig(use="test"))
+
+
+def _make_app() -> FastAPI:
+    """Build a memory-router app pre-populated with a minimal AppConfig."""
+    app = FastAPI()
+    app.state.config = _TEST_APP_CONFIG
+    app.include_router(memory.router)
+    return app
 
 
 def _sample_memory(facts: list[dict] | None = None) -> dict:
@@ -25,8 +37,7 @@ def _sample_memory(facts: list[dict] | None = None) -> dict:
 
 
 def test_export_memory_route_returns_current_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     exported_memory = _sample_memory(
         facts=[
             {
@@ -49,8 +60,7 @@ def test_export_memory_route_returns_current_memory() -> None:
 
 
 def test_import_memory_route_returns_imported_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     imported_memory = _sample_memory(
         facts=[
             {
@@ -73,8 +83,7 @@ def test_import_memory_route_returns_imported_memory() -> None:
 
 
 def test_export_memory_route_preserves_source_error() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     exported_memory = _sample_memory(
         facts=[
             {
@@ -98,8 +107,7 @@ def test_export_memory_route_preserves_source_error() -> None:
 
 
 def test_import_memory_route_preserves_source_error() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     imported_memory = _sample_memory(
         facts=[
             {
@@ -123,8 +131,7 @@ def test_import_memory_route_preserves_source_error() -> None:
 
 
 def test_clear_memory_route_returns_cleared_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
 
     with patch("app.gateway.routers.memory.clear_memory_data", return_value=_sample_memory()):
         with TestClient(app) as client:
@@ -135,8 +142,7 @@ def test_clear_memory_route_returns_cleared_memory() -> None:
 
 
 def test_create_memory_fact_route_returns_updated_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     updated_memory = _sample_memory(
         facts=[
             {
@@ -166,8 +172,7 @@ def test_create_memory_fact_route_returns_updated_memory() -> None:
 
 
 def test_delete_memory_fact_route_returns_updated_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     updated_memory = _sample_memory(
         facts=[
             {
@@ -190,8 +195,7 @@ def test_delete_memory_fact_route_returns_updated_memory() -> None:
 
 
 def test_delete_memory_fact_route_returns_404_for_missing_fact() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
 
     with patch("app.gateway.routers.memory.delete_memory_fact", side_effect=KeyError("fact_missing")):
         with TestClient(app) as client:
@@ -202,8 +206,7 @@ def test_delete_memory_fact_route_returns_404_for_missing_fact() -> None:
 
 
 def test_update_memory_fact_route_returns_updated_memory() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     updated_memory = _sample_memory(
         facts=[
             {
@@ -233,8 +236,7 @@ def test_update_memory_fact_route_returns_updated_memory() -> None:
 
 
 def test_update_memory_fact_route_preserves_omitted_fields() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
     updated_memory = _sample_memory(
         facts=[
             {
@@ -258,18 +260,18 @@ def test_update_memory_fact_route_preserves_omitted_fields() -> None:
             )
 
     assert response.status_code == 200
-    update_fact.assert_called_once_with(
-        fact_id="fact_edit",
-        content="User prefers spaces",
-        category=None,
-        confidence=None,
-    )
+    assert update_fact.call_count == 1
+    call_kwargs = update_fact.call_args.kwargs
+    assert call_kwargs.get("fact_id") == "fact_edit"
+    assert call_kwargs.get("content") == "User prefers spaces"
+    assert call_kwargs.get("category") is None
+    assert call_kwargs.get("confidence") is None
+    assert "user_id" in call_kwargs
     assert response.json()["facts"] == updated_memory["facts"]
 
 
 def test_update_memory_fact_route_returns_404_for_missing_fact() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
 
     with patch("app.gateway.routers.memory.update_memory_fact", side_effect=KeyError("fact_missing")):
         with TestClient(app) as client:
@@ -287,8 +289,7 @@ def test_update_memory_fact_route_returns_404_for_missing_fact() -> None:
 
 
 def test_update_memory_fact_route_returns_specific_error_for_invalid_confidence() -> None:
-    app = FastAPI()
-    app.include_router(memory.router)
+    app = _make_app()
 
     with patch("app.gateway.routers.memory.update_memory_fact", side_effect=ValueError("confidence")):
         with TestClient(app) as client: