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/tools/tools.py

@@ -2,7 +2,7 @@ import logging
 
 from langchain.tools import BaseTool
 
-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
 from deerflow.reflection import resolve_variable
 from deerflow.sandbox.security import is_host_bash_allowed
 from deerflow.tools.builtins import ask_clarification_tool, present_file_tool, task_tool, view_image_tool
@@ -37,6 +37,8 @@ def get_available_tools(
     include_mcp: bool = True,
     model_name: str | None = None,
     subagent_enabled: bool = False,
+    *,
+    app_config: AppConfig,
 ) -> list[BaseTool]:
     """Get all available tools from config.
 
@@ -48,11 +50,12 @@ def get_available_tools(
         include_mcp: Whether to include tools from MCP servers (default: True).
         model_name: Optional model name to determine if vision tools should be included.
         subagent_enabled: Whether to include subagent tools (task, task_status).
+        app_config: Application config — required.
 
     Returns:
         List of available tools.
     """
-    config = get_app_config()
+    config = app_config
     tool_configs = [tool for tool in config.tools if groups is None or tool.group in groups]
 
     # Do not expose host bash by default when LocalSandboxProvider is active.
@@ -138,10 +141,9 @@ def get_available_tools(
     # Add invoke_acp_agent tool if any ACP agents are configured
     acp_tools: list[BaseTool] = []
     try:
-        from deerflow.config.acp_config import get_acp_agents
         from deerflow.tools.builtins.invoke_acp_agent_tool import build_invoke_acp_agent_tool
 
-        acp_agents = get_acp_agents()
+        acp_agents = config.acp_agents
         if acp_agents:
             acp_tools.append(build_invoke_acp_agent_tool(acp_agents))
             logger.info(f"Including invoke_acp_agent tool ({len(acp_agents)} agent(s): {list(acp_agents.keys())})")