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/builtins/task_tool.py

@@ -11,6 +11,7 @@ from langgraph.config import get_stream_writer
 from langgraph.typing import ContextT
 
 from deerflow.agents.thread_state import ThreadState
+from deerflow.config.deer_flow_context import resolve_context
 from deerflow.sandbox.security import LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE, is_host_bash_allowed
 from deerflow.subagents import SubagentExecutor, get_available_subagent_names, get_subagent_config
 from deerflow.subagents.executor import SubagentStatus, cleanup_background_task, get_background_task_result, request_cancel_background_task
@@ -74,14 +75,15 @@ async def task_tool(
         subagent_type: The type of subagent to use. ALWAYS PROVIDE THIS PARAMETER THIRD.
         max_turns: Optional maximum number of agent turns. Defaults to subagent's configured max.
     """
-    available_subagent_names = get_available_subagent_names()
+    ctx = resolve_context(runtime)
+    available_subagent_names = get_available_subagent_names(ctx.app_config)
 
     # Get subagent configuration
-    config = get_subagent_config(subagent_type)
+    config = get_subagent_config(subagent_type, ctx.app_config)
     if config is None:
         available = ", ".join(available_subagent_names)
         return f"Error: Unknown subagent type '{subagent_type}'. Available: {available}"
-    if subagent_type == "bash" and not is_host_bash_allowed():
+    if subagent_type == "bash" and not is_host_bash_allowed(ctx.app_config):
         return f"Error: {LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE}"
 
     # Build config overrides
@@ -105,9 +107,7 @@ async def task_tool(
     if runtime is not None:
         sandbox_state = runtime.state.get("sandbox")
         thread_data = runtime.state.get("thread_data")
-        thread_id = runtime.context.get("thread_id") if runtime.context else None
-        if thread_id is None:
-            thread_id = runtime.config.get("configurable", {}).get("thread_id")
+        thread_id = runtime.context.thread_id
 
         # Try to get parent model from configurable
         metadata = runtime.config.get("metadata", {})
@@ -131,12 +131,13 @@ async def task_tool(
     parent_tool_groups = metadata.get("tool_groups")
 
     # Subagents should not have subagent tools enabled (prevent recursive nesting)
-    tools = get_available_tools(model_name=parent_model, groups=parent_tool_groups, subagent_enabled=False)
+    tools = get_available_tools(model_name=parent_model, groups=parent_tool_groups, subagent_enabled=False, app_config=ctx.app_config)
 
     # Create executor
     executor = SubagentExecutor(
         config=config,
         tools=tools,
+        app_config=ctx.app_config,
         parent_model=parent_model,
         sandbox_state=sandbox_state,
         thread_data=thread_data,