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/community/infoquest/tools.py

@@ -1,6 +1,7 @@
-from langchain.tools import tool
+from langchain.tools import ToolRuntime, tool
 
-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
+from deerflow.config.deer_flow_context import resolve_context
 from deerflow.utils.readability import ReadabilityExtractor
 
 from .infoquest_client import InfoQuestClient
@@ -8,13 +9,13 @@ from .infoquest_client import InfoQuestClient
 readability_extractor = ReadabilityExtractor()
 
 
-def _get_infoquest_client() -> InfoQuestClient:
-    search_config = get_app_config().get_tool_config("web_search")
+def _get_infoquest_client(app_config: AppConfig) -> InfoQuestClient:
+    search_config = app_config.get_tool_config("web_search")
     search_time_range = -1
     if search_config is not None and "search_time_range" in search_config.model_extra:
         search_time_range = search_config.model_extra.get("search_time_range")
 
-    fetch_config = get_app_config().get_tool_config("web_fetch")
+    fetch_config = app_config.get_tool_config("web_fetch")
     fetch_time = -1
     if fetch_config is not None and "fetch_time" in fetch_config.model_extra:
         fetch_time = fetch_config.model_extra.get("fetch_time")
@@ -25,7 +26,7 @@ def _get_infoquest_client() -> InfoQuestClient:
     if fetch_config is not None and "navigation_timeout" in fetch_config.model_extra:
         navigation_timeout = fetch_config.model_extra.get("navigation_timeout")
 
-    image_search_config = get_app_config().get_tool_config("image_search")
+    image_search_config = app_config.get_tool_config("image_search")
     image_search_time_range = -1
     if image_search_config is not None and "image_search_time_range" in image_search_config.model_extra:
         image_search_time_range = image_search_config.model_extra.get("image_search_time_range")
@@ -44,19 +45,18 @@ def _get_infoquest_client() -> InfoQuestClient:
 
 
 @tool("web_search", parse_docstring=True)
-def web_search_tool(query: str) -> str:
+def web_search_tool(query: str, runtime: ToolRuntime) -> str:
     """Search the web.
 
     Args:
         query: The query to search for.
     """
-
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
     return client.web_search(query)
 
 
 @tool("web_fetch", parse_docstring=True)
-def web_fetch_tool(url: str) -> str:
+def web_fetch_tool(url: str, runtime: ToolRuntime) -> str:
     """Fetch the contents of a web page at a given URL.
     Only fetch EXACT URLs that have been provided directly by the user or have been returned in results from the web_search and web_fetch tools.
     This tool can NOT access content that requires authentication, such as private Google Docs or pages behind login walls.
@@ -66,7 +66,7 @@ def web_fetch_tool(url: str) -> str:
     Args:
         url: The URL to fetch the contents of.
     """
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
     result = client.fetch(url)
     if result.startswith("Error: "):
         return result
@@ -75,7 +75,7 @@ def web_fetch_tool(url: str) -> str:
 
 
 @tool("image_search", parse_docstring=True)
-def image_search_tool(query: str) -> str:
+def image_search_tool(query: str, runtime: ToolRuntime) -> str:
     """Search for images online. Use this tool BEFORE image generation to find reference images for characters, portraits, objects, scenes, or any content requiring visual accuracy.
 
     **When to use:**
@@ -89,5 +89,5 @@ def image_search_tool(query: str) -> str:
     Args:
         query: The query to search for images.
     """
-    client = _get_infoquest_client()
+    client = _get_infoquest_client(resolve_context(runtime).app_config)
     return client.image_search(query)