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/packages/harness/deerflow/subagents/executor.py

@@ -17,6 +17,7 @@ from langchain_core.messages import AIMessage, HumanMessage, SystemMessage
 from langchain_core.runnables import RunnableConfig
 
 from deerflow.agents.thread_state import SandboxState, ThreadDataState, ThreadState
+from deerflow.config.app_config import AppConfig
 from deerflow.models import create_chat_model
 from deerflow.subagents.config import SubagentConfig
 
@@ -132,24 +133,16 @@ class SubagentExecutor:
         self,
         config: SubagentConfig,
         tools: list[BaseTool],
+        app_config: AppConfig,
         parent_model: str | None = None,
         sandbox_state: SandboxState | None = None,
         thread_data: ThreadDataState | None = None,
         thread_id: str | None = None,
         trace_id: str | None = None,
     ):
-        """Initialize the executor.
-
-        Args:
-            config: Subagent configuration.
-            tools: List of all available tools (will be filtered).
-            parent_model: The parent agent's model name for inheritance.
-            sandbox_state: Sandbox state from parent agent.
-            thread_data: Thread data from parent agent.
-            thread_id: Thread ID for sandbox operations.
-            trace_id: Trace ID from parent for distributed tracing.
-        """
+        """Initialize the executor."""
         self.config = config
+        self.app_config = app_config
         self.parent_model = parent_model
         self.sandbox_state = sandbox_state
         self.thread_data = thread_data
@@ -169,7 +162,7 @@ class SubagentExecutor:
     def _create_agent(self):
         """Create the agent instance."""
         model_name = _get_model_name(self.config, self.parent_model)
-        model = create_chat_model(name=model_name, thinking_enabled=False)
+        model = create_chat_model(name=model_name, thinking_enabled=False, app_config=self.app_config)
 
         from deerflow.agents.middlewares.tool_error_handling_middleware import build_subagent_runtime_middlewares