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_skills_custom_router.py

@@ -7,6 +7,9 @@ from fastapi import FastAPI
 from fastapi.testclient import TestClient
 
 from app.gateway.routers import skills as skills_router
+from deerflow.config.app_config import AppConfig
+from deerflow.config.extensions_config import ExtensionsConfig
+from deerflow.config.sandbox_config import SandboxConfig
 from deerflow.skills.manager import get_skill_history_file
 from deerflow.skills.types import Skill
 
@@ -44,17 +47,16 @@ def test_custom_skills_router_lifecycle(monkeypatch, tmp_path):
         skills=SimpleNamespace(get_skills_path=lambda: skills_root, container_path="/mnt/skills"),
         skill_evolution=SimpleNamespace(enabled=True, moderation_model_name=None),
     )
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-    monkeypatch.setattr("deerflow.skills.manager.get_app_config", lambda: config)
     monkeypatch.setattr("app.gateway.routers.skills.scan_skill_content", lambda *args, **kwargs: _async_scan("allow", "ok"))
     refresh_calls = []
 
-    async def _refresh():
+    async def _refresh(*a, **k):
         refresh_calls.append("refresh")
 
     monkeypatch.setattr("app.gateway.routers.skills.refresh_skills_system_prompt_cache_async", _refresh)
 
     app = FastAPI()
+    app.state.config = config
     app.include_router(skills_router.router)
 
     with TestClient(app) as client:
@@ -94,14 +96,12 @@ def test_custom_skill_rollback_blocked_by_scanner(monkeypatch, tmp_path):
         skills=SimpleNamespace(get_skills_path=lambda: skills_root, container_path="/mnt/skills"),
         skill_evolution=SimpleNamespace(enabled=True, moderation_model_name=None),
     )
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-    monkeypatch.setattr("deerflow.skills.manager.get_app_config", lambda: config)
-    get_skill_history_file("demo-skill").write_text(
+    get_skill_history_file("demo-skill", config).write_text(
         '{"action":"human_edit","prev_content":' + json.dumps(original_content) + ',"new_content":' + json.dumps(edited_content) + "}\n",
         encoding="utf-8",
     )
 
-    async def _refresh():
+    async def _refresh(*a, **k):
         return None
 
     monkeypatch.setattr("app.gateway.routers.skills.refresh_skills_system_prompt_cache_async", _refresh)
@@ -114,6 +114,7 @@ def test_custom_skill_rollback_blocked_by_scanner(monkeypatch, tmp_path):
     monkeypatch.setattr("app.gateway.routers.skills.scan_skill_content", _scan)
 
     app = FastAPI()
+    app.state.config = config
     app.include_router(skills_router.router)
 
     with TestClient(app) as client:
@@ -136,17 +137,16 @@ def test_custom_skill_delete_preserves_history_and_allows_restore(monkeypatch, t
         skills=SimpleNamespace(get_skills_path=lambda: skills_root, container_path="/mnt/skills"),
         skill_evolution=SimpleNamespace(enabled=True, moderation_model_name=None),
     )
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-    monkeypatch.setattr("deerflow.skills.manager.get_app_config", lambda: config)
     monkeypatch.setattr("app.gateway.routers.skills.scan_skill_content", lambda *args, **kwargs: _async_scan("allow", "ok"))
     refresh_calls = []
 
-    async def _refresh():
+    async def _refresh(*a, **k):
         refresh_calls.append("refresh")
 
     monkeypatch.setattr("app.gateway.routers.skills.refresh_skills_system_prompt_cache_async", _refresh)
 
     app = FastAPI()
+    app.state.config = config
     app.include_router(skills_router.router)
 
     with TestClient(app) as client:
@@ -238,23 +238,25 @@ def test_update_skill_refreshes_prompt_cache_before_return(monkeypatch, tmp_path
     enabled_state = {"value": True}
     refresh_calls = []
 
-    def _load_skills(*, enabled_only: bool):
+    def _load_skills(*a, enabled_only: bool = False, **k):
         skill = _make_skill("demo-skill", enabled=enabled_state["value"])
         if enabled_only and not skill.enabled:
             return []
         return [skill]
 
-    async def _refresh():
+    async def _refresh(*a, **k):
         refresh_calls.append("refresh")
         enabled_state["value"] = False
 
+    _app_cfg = AppConfig(sandbox=SandboxConfig(use="test"), extensions=ExtensionsConfig(mcp_servers={}, skills={}))
+
     monkeypatch.setattr("app.gateway.routers.skills.load_skills", _load_skills)
-    monkeypatch.setattr("app.gateway.routers.skills.get_extensions_config", lambda: SimpleNamespace(mcp_servers={}, skills={}))
-    monkeypatch.setattr("app.gateway.routers.skills.reload_extensions_config", lambda: None)
+    monkeypatch.setattr(AppConfig, "from_file", staticmethod(lambda: _app_cfg))
     monkeypatch.setattr(skills_router.ExtensionsConfig, "resolve_config_path", staticmethod(lambda: config_path))
     monkeypatch.setattr("app.gateway.routers.skills.refresh_skills_system_prompt_cache_async", _refresh)
 
     app = FastAPI()
+    app.state.config = _app_cfg
     app.include_router(skills_router.router)
 
     with TestClient(app) as client: