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/tests/test_lead_agent_prompt.py

@@ -4,25 +4,23 @@ from types import SimpleNamespace
 import anyio
 
 from deerflow.agents.lead_agent import prompt as prompt_module
+from deerflow.config.app_config import AppConfig
 from deerflow.skills.types import Skill
 
 
-def test_build_custom_mounts_section_returns_empty_when_no_mounts(monkeypatch):
+def test_build_custom_mounts_section_returns_empty_when_no_mounts():
     config = SimpleNamespace(sandbox=SimpleNamespace(mounts=[]))
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-
-    assert prompt_module._build_custom_mounts_section() == ""
+    assert prompt_module._build_custom_mounts_section(config) == ""
 
 
-def test_build_custom_mounts_section_lists_configured_mounts(monkeypatch):
+def test_build_custom_mounts_section_lists_configured_mounts():
     mounts = [
         SimpleNamespace(container_path="/home/user/shared", read_only=False),
         SimpleNamespace(container_path="/mnt/reference", read_only=True),
     ]
     config = SimpleNamespace(sandbox=SimpleNamespace(mounts=mounts))
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
 
-    section = prompt_module._build_custom_mounts_section()
+    section = prompt_module._build_custom_mounts_section(config)
 
     assert "**Custom Mounted Directories:**" in section
     assert "`/home/user/shared`" in section
@@ -36,15 +34,15 @@ def test_apply_prompt_template_includes_custom_mounts(monkeypatch):
     config = SimpleNamespace(
         sandbox=SimpleNamespace(mounts=mounts),
         skills=SimpleNamespace(container_path="/mnt/skills"),
+        skill_evolution=SimpleNamespace(enabled=False),
     )
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-    monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda: [])
-    monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None: "")
+    monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda *a, **k: [])
+    monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda app_config: "")
+    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda app_config: "")
+    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda app_config, agent_name=None: "")
     monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
 
-    prompt = prompt_module.apply_prompt_template()
+    prompt = prompt_module.apply_prompt_template(config)
 
     assert "`/home/user/shared`" in prompt
     assert "Custom Mounted Directories" in prompt
@@ -54,15 +52,15 @@ def test_apply_prompt_template_includes_relative_path_guidance(monkeypatch):
     config = SimpleNamespace(
         sandbox=SimpleNamespace(mounts=[]),
         skills=SimpleNamespace(container_path="/mnt/skills"),
+        skill_evolution=SimpleNamespace(enabled=False),
     )
-    monkeypatch.setattr("deerflow.config.get_app_config", lambda: config)
-    monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda: [])
-    monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda: "")
-    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda agent_name=None: "")
+    monkeypatch.setattr(prompt_module, "_get_enabled_skills", lambda *a, **k: [])
+    monkeypatch.setattr(prompt_module, "get_deferred_tools_prompt_section", lambda app_config: "")
+    monkeypatch.setattr(prompt_module, "_build_acp_section", lambda app_config: "")
+    monkeypatch.setattr(prompt_module, "_get_memory_context", lambda app_config, agent_name=None: "")
     monkeypatch.setattr(prompt_module, "get_agent_soul", lambda agent_name=None: "")
 
-    prompt = prompt_module.apply_prompt_template()
+    prompt = prompt_module.apply_prompt_template(config)
 
     assert "Treat `/mnt/user-data/workspace` as your default current working directory" in prompt
     assert "`hello.txt`, `../uploads/data.csv`, and `../outputs/report.md`" in prompt
@@ -83,7 +81,7 @@ def test_refresh_skills_system_prompt_cache_async_reloads_immediately(monkeypatc
         )
 
     state = {"skills": [make_skill("first-skill")]}
-    monkeypatch.setattr(prompt_module, "load_skills", lambda enabled_only=True: list(state["skills"]))
+    monkeypatch.setattr(prompt_module, "load_skills", lambda *a, **kwargs: list(state["skills"]))
     prompt_module._reset_skills_system_prompt_cache_state()
 
     try:
@@ -119,7 +117,7 @@ def test_clear_cache_does_not_spawn_parallel_refresh_workers(monkeypatch, tmp_pa
             enabled=True,
         )
 
-    def fake_load_skills(enabled_only=True):
+    def fake_load_skills(*a, **kwargs):
         nonlocal active_loads, max_active_loads, call_count
         with lock:
             active_loads += 1
@@ -156,7 +154,7 @@ def test_clear_cache_does_not_spawn_parallel_refresh_workers(monkeypatch, tmp_pa
 
 def test_warm_enabled_skills_cache_logs_on_timeout(monkeypatch, caplog):
     event = threading.Event()
-    monkeypatch.setattr(prompt_module, "_ensure_enabled_skills_cache", lambda: event)
+    monkeypatch.setattr(prompt_module, "_ensure_enabled_skills_cache", lambda *a, **k: event)
 
     with caplog.at_level("WARNING"):
         warmed = prompt_module.warm_enabled_skills_cache(timeout_seconds=0.01)