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_invoke_acp_agent_tool.py

@@ -6,7 +6,7 @@ from types import SimpleNamespace
 import pytest
 
 from deerflow.config.acp_config import ACPAgentConfig
-from deerflow.config.extensions_config import ExtensionsConfig, McpServerConfig, set_extensions_config
+from deerflow.config.extensions_config import ExtensionsConfig, McpServerConfig
 from deerflow.tools.builtins.invoke_acp_agent_tool import (
     _build_acp_mcp_servers,
     _build_mcp_servers,
@@ -18,7 +18,6 @@ from deerflow.tools.tools import get_available_tools
 
 
 def test_build_mcp_servers_filters_disabled_and_maps_transports():
-    set_extensions_config(ExtensionsConfig(mcp_servers={"stale": McpServerConfig(enabled=True, type="stdio", command="echo")}, skills={}))
     fresh_config = ExtensionsConfig(
         mcp_servers={
             "stdio": McpServerConfig(enabled=True, type="stdio", command="npx", args=["srv"]),
@@ -40,11 +39,9 @@ def test_build_mcp_servers_filters_disabled_and_maps_transports():
         }
     finally:
         monkeypatch.undo()
-        set_extensions_config(ExtensionsConfig(mcp_servers={}, skills={}))
 
 
 def test_build_acp_mcp_servers_formats_list_payload():
-    set_extensions_config(ExtensionsConfig(mcp_servers={"stale": McpServerConfig(enabled=True, type="stdio", command="echo")}, skills={}))
     fresh_config = ExtensionsConfig(
         mcp_servers={
             "stdio": McpServerConfig(enabled=True, type="stdio", command="npx", args=["srv"], env={"FOO": "bar"}),
@@ -77,7 +74,6 @@ def test_build_acp_mcp_servers_formats_list_payload():
         ]
     finally:
         monkeypatch.undo()
-        set_extensions_config(ExtensionsConfig(mcp_servers={}, skills={}))
 
 
 def test_build_permission_response_prefers_allow_once():
@@ -152,8 +148,10 @@ def test_get_work_dir_uses_base_dir_when_no_thread_id(monkeypatch, tmp_path):
 def test_get_work_dir_uses_per_thread_path_when_thread_id_given(monkeypatch, tmp_path):
     """P1.1: _get_work_dir(thread_id) uses {base_dir}/threads/{thread_id}/acp-workspace/."""
     from deerflow.config import paths as paths_module
+    from deerflow.runtime import user_context as uc_module
 
     monkeypatch.setattr(paths_module, "get_paths", lambda: paths_module.Paths(base_dir=tmp_path))
+    monkeypatch.setattr(uc_module, "get_effective_user_id", lambda: None)
     result = _get_work_dir("thread-abc-123")
     expected = tmp_path / "threads" / "thread-abc-123" / "acp-workspace"
     assert result == str(expected)
@@ -310,8 +308,10 @@ async def test_invoke_acp_agent_uses_fixed_acp_workspace(monkeypatch, tmp_path):
 async def test_invoke_acp_agent_uses_per_thread_workspace_when_thread_id_in_config(monkeypatch, tmp_path):
     """P1.1: When thread_id is in the RunnableConfig, ACP agent uses per-thread workspace."""
     from deerflow.config import paths as paths_module
+    from deerflow.runtime import user_context as uc_module
 
     monkeypatch.setattr(paths_module, "get_paths", lambda: paths_module.Paths(base_dir=tmp_path))
+    monkeypatch.setattr(uc_module, "get_effective_user_id", lambda: None)
 
     monkeypatch.setattr(
         "deerflow.config.extensions_config.ExtensionsConfig.from_file",
@@ -665,31 +665,23 @@ async def test_invoke_acp_agent_passes_none_env_when_not_configured(monkeypatch,
 
 
 def test_get_available_tools_includes_invoke_acp_agent_when_agents_configured(monkeypatch):
-    from deerflow.config.acp_config import load_acp_config_from_dict
-
-    load_acp_config_from_dict(
-        {
-            "codex": {
-                "command": "codex-acp",
-                "args": [],
-                "description": "Codex CLI",
-            }
-        }
-    )
-
     fake_config = SimpleNamespace(
         tools=[],
         models=[],
         tool_search=SimpleNamespace(enabled=False),
+        acp_agents={
+            "codex": ACPAgentConfig(
+                command="codex-acp",
+                args=[],
+                description="Codex CLI",
+            )
+        },
         get_model_config=lambda name: None,
     )
-    monkeypatch.setattr("deerflow.tools.tools.get_app_config", lambda: fake_config)
     monkeypatch.setattr(
         "deerflow.config.extensions_config.ExtensionsConfig.from_file",
         classmethod(lambda cls: ExtensionsConfig(mcp_servers={}, skills={})),
     )
 
-    tools = get_available_tools(include_mcp=True, subagent_enabled=False)
+    tools = get_available_tools(include_mcp=True, subagent_enabled=False, app_config=fake_config)
     assert "invoke_acp_agent" in [tool.name for tool in tools]
-
-    load_acp_config_from_dict({})