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_sandbox_search_tools.py

@@ -14,6 +14,10 @@ def _make_runtime(tmp_path):
     workspace.mkdir()
     uploads.mkdir()
     outputs.mkdir()
+    from deerflow.config.app_config import AppConfig
+    from deerflow.config.deer_flow_context import DeerFlowContext
+    from deerflow.config.sandbox_config import SandboxConfig
+
     return SimpleNamespace(
         state={
             "sandbox": {"sandbox_id": "local"},
@@ -23,7 +27,10 @@ def _make_runtime(tmp_path):
                 "outputs_path": str(outputs),
             },
         },
-        context={"thread_id": "thread-1"},
+        context=DeerFlowContext(
+            app_config=AppConfig(sandbox=SandboxConfig(use="test")),
+            thread_id="thread-1",
+        ),
     )
 
 
@@ -103,8 +110,6 @@ def test_grep_tool_truncates_results(tmp_path, monkeypatch) -> None:
     (workspace / "main.py").write_text("TODO one\nTODO two\nTODO three\n", encoding="utf-8")
 
     monkeypatch.setattr("deerflow.sandbox.tools.ensure_sandbox_initialized", lambda runtime: LocalSandbox(id="local"))
-    # Prevent config.yaml tool config from overriding the caller-supplied max_results=2.
-    monkeypatch.setattr("deerflow.sandbox.tools.get_app_config", lambda: SimpleNamespace(get_tool_config=lambda name: None))
 
     result = grep_tool.func(
         runtime=runtime,
@@ -324,10 +329,6 @@ def test_glob_tool_honors_smaller_requested_max_results(tmp_path, monkeypatch) -
     (workspace / "c.py").write_text("print('c')\n", encoding="utf-8")
 
     monkeypatch.setattr("deerflow.sandbox.tools.ensure_sandbox_initialized", lambda runtime: LocalSandbox(id="local"))
-    monkeypatch.setattr(
-        "deerflow.sandbox.tools.get_app_config",
-        lambda: SimpleNamespace(get_tool_config=lambda name: SimpleNamespace(model_extra={"max_results": 50})),
-    )
 
     result = glob_tool.func(
         runtime=runtime,