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/app/gateway/routers/agents.py

@@ -5,11 +5,12 @@ import re
 import shutil
 
 import yaml
-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, Depends, HTTPException
 from pydantic import BaseModel, Field
 
-from deerflow.config.agents_api_config import get_agents_api_config
+from app.gateway.deps import get_config
 from deerflow.config.agents_config import AgentConfig, list_custom_agents, load_agent_config, load_agent_soul
+from deerflow.config.app_config import AppConfig
 from deerflow.config.paths import get_paths
 
 logger = logging.getLogger(__name__)
@@ -77,9 +78,9 @@ def _normalize_agent_name(name: str) -> str:
     return name.lower()
 
 
-def _require_agents_api_enabled() -> None:
+def _require_agents_api_enabled(app_config: AppConfig) -> None:
     """Reject access unless the custom-agent management API is explicitly enabled."""
-    if not get_agents_api_config().enabled:
+    if not app_config.agents_api.enabled:
         raise HTTPException(
             status_code=403,
             detail=("Custom-agent management API is disabled. Set agents_api.enabled=true to expose agent and user-profile routes over HTTP."),
@@ -108,13 +109,13 @@ def _agent_config_to_response(agent_cfg: AgentConfig, include_soul: bool = False
     summary="List Custom Agents",
     description="List all custom agents available in the agents directory, including their soul content.",
 )
-async def list_agents() -> AgentsListResponse:
+async def list_agents(app_config: AppConfig = Depends(get_config)) -> AgentsListResponse:
     """List all custom agents.
 
     Returns:
         List of all custom agents with their metadata and soul content.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
 
     try:
         agents = list_custom_agents()
@@ -141,7 +142,7 @@ async def check_agent_name(name: str) -> dict:
     Raises:
         HTTPException: 422 if the name is invalid.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
     _validate_agent_name(name)
     normalized = _normalize_agent_name(name)
     available = not get_paths().agent_dir(normalized).exists()
@@ -154,7 +155,7 @@ async def check_agent_name(name: str) -> dict:
     summary="Get Custom Agent",
     description="Retrieve details and SOUL.md content for a specific custom agent.",
 )
-async def get_agent(name: str) -> AgentResponse:
+async def get_agent(name: str, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
     """Get a specific custom agent by name.
 
     Args:
@@ -166,7 +167,7 @@ async def get_agent(name: str) -> AgentResponse:
     Raises:
         HTTPException: 404 if agent not found.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
     _validate_agent_name(name)
     name = _normalize_agent_name(name)
 
@@ -187,7 +188,7 @@ async def get_agent(name: str) -> AgentResponse:
     summary="Create Custom Agent",
     description="Create a new custom agent with its config and SOUL.md.",
 )
-async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
+async def create_agent_endpoint(request: AgentCreateRequest, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
     """Create a new custom agent.
 
     Args:
@@ -199,7 +200,7 @@ async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
     Raises:
         HTTPException: 409 if agent already exists, 422 if name is invalid.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
     _validate_agent_name(request.name)
     normalized_name = _normalize_agent_name(request.name)
 
@@ -251,7 +252,7 @@ async def create_agent_endpoint(request: AgentCreateRequest) -> AgentResponse:
     summary="Update Custom Agent",
     description="Update an existing custom agent's config and/or SOUL.md.",
 )
-async def update_agent(name: str, request: AgentUpdateRequest) -> AgentResponse:
+async def update_agent(name: str, request: AgentUpdateRequest, app_config: AppConfig = Depends(get_config)) -> AgentResponse:
     """Update an existing custom agent.
 
     Args:
@@ -264,7 +265,7 @@ async def update_agent(name: str, request: AgentUpdateRequest) -> AgentResponse:
     Raises:
         HTTPException: 404 if agent not found.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
     _validate_agent_name(name)
     name = _normalize_agent_name(name)
 
@@ -342,13 +343,13 @@ class UserProfileUpdateRequest(BaseModel):
     summary="Get User Profile",
     description="Read the global USER.md file that is injected into all custom agents.",
 )
-async def get_user_profile() -> UserProfileResponse:
+async def get_user_profile(app_config: AppConfig = Depends(get_config)) -> UserProfileResponse:
     """Return the current USER.md content.
 
     Returns:
         UserProfileResponse with content=None if USER.md does not exist yet.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
 
     try:
         user_md_path = get_paths().user_md_file
@@ -367,7 +368,7 @@ async def get_user_profile() -> UserProfileResponse:
     summary="Update User Profile",
     description="Write the global USER.md file that is injected into all custom agents.",
 )
-async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileResponse:
+async def update_user_profile(request: UserProfileUpdateRequest, app_config: AppConfig = Depends(get_config)) -> UserProfileResponse:
     """Create or overwrite the global USER.md.
 
     Args:
@@ -376,7 +377,7 @@ async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileR
     Returns:
         UserProfileResponse with the saved content.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
 
     try:
         paths = get_paths()
@@ -395,7 +396,7 @@ async def update_user_profile(request: UserProfileUpdateRequest) -> UserProfileR
     summary="Delete Custom Agent",
     description="Delete a custom agent and all its files (config, SOUL.md, memory).",
 )
-async def delete_agent(name: str) -> None:
+async def delete_agent(name: str, app_config: AppConfig = Depends(get_config)) -> None:
     """Delete a custom agent.
 
     Args:
@@ -404,7 +405,7 @@ async def delete_agent(name: str) -> None:
     Raises:
         HTTPException: 404 if agent not found.
     """
-    _require_agents_api_enabled()
+    _require_agents_api_enabled(app_config)
     _validate_agent_name(name)
     name = _normalize_agent_name(name)