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_acp_config.py

@@ -2,21 +2,27 @@
 
 import json
 
+import pytest
 import pytest
 import yaml
+
+pytestmark = pytest.mark.real_from_file
 from pydantic import ValidationError
 
-from deerflow.config.acp_config import ACPAgentConfig, get_acp_agents, load_acp_config_from_dict
+from deerflow.config.acp_config import ACPAgentConfig
 from deerflow.config.app_config import AppConfig
+from deerflow.config.sandbox_config import SandboxConfig
 
 
-def setup_function():
-    """Reset ACP config before each test."""
-    load_acp_config_from_dict({})
+def _make_config(acp_agents: dict | None = None) -> AppConfig:
+    return AppConfig(
+        sandbox=SandboxConfig(use="test"),
+        acp_agents={name: ACPAgentConfig(**cfg) for name, cfg in (acp_agents or {}).items()},
+    )
 
 
-def test_load_acp_config_sets_agents():
-    load_acp_config_from_dict(
+def test_acp_agents_via_app_config():
+    cfg = _make_config(
         {
             "claude_code": {
                 "command": "claude-code-acp",
@@ -26,39 +32,33 @@ def test_load_acp_config_sets_agents():
             }
         }
     )
-    agents = get_acp_agents()
+    agents = cfg.acp_agents
     assert "claude_code" in agents
     assert agents["claude_code"].command == "claude-code-acp"
     assert agents["claude_code"].description == "Claude Code for coding tasks"
     assert agents["claude_code"].model is None
 
 
-def test_load_acp_config_multiple_agents():
-    load_acp_config_from_dict(
+def test_multiple_agents():
+    cfg = _make_config(
         {
             "claude_code": {"command": "claude-code-acp", "args": [], "description": "Claude Code"},
             "codex": {"command": "codex-acp", "args": ["--flag"], "description": "Codex CLI"},
         }
     )
-    agents = get_acp_agents()
+    agents = cfg.acp_agents
     assert len(agents) == 2
     assert agents["codex"].args == ["--flag"]
 
 
-def test_load_acp_config_empty_clears_agents():
-    load_acp_config_from_dict({"agent": {"command": "cmd", "args": [], "description": "desc"}})
-    assert len(get_acp_agents()) == 1
-
-    load_acp_config_from_dict({})
-    assert len(get_acp_agents()) == 0
+def test_empty_acp_agents():
+    cfg = _make_config({})
+    assert cfg.acp_agents == {}
 
 
-def test_load_acp_config_none_clears_agents():
-    load_acp_config_from_dict({"agent": {"command": "cmd", "args": [], "description": "desc"}})
-    assert len(get_acp_agents()) == 1
-
-    load_acp_config_from_dict(None)
-    assert get_acp_agents() == {}
+def test_default_acp_agents_empty():
+    cfg = AppConfig(sandbox=SandboxConfig(use="test"))
+    assert cfg.acp_agents == {}
 
 
 def test_acp_agent_config_defaults():
@@ -79,8 +79,8 @@ def test_acp_agent_config_env_default_is_empty():
     assert cfg.env == {}
 
 
-def test_load_acp_config_preserves_env():
-    load_acp_config_from_dict(
+def test_acp_agent_preserves_env():
+    cfg = _make_config(
         {
             "codex": {
                 "command": "codex-acp",
@@ -90,8 +90,7 @@ def test_load_acp_config_preserves_env():
             }
         }
     )
-    cfg = get_acp_agents()["codex"]
-    assert cfg.env == {"OPENAI_API_KEY": "$OPENAI_API_KEY", "FOO": "bar"}
+    assert cfg.acp_agents["codex"].env == {"OPENAI_API_KEY": "$OPENAI_API_KEY", "FOO": "bar"}
 
 
 def test_acp_agent_config_with_model():
@@ -115,13 +114,7 @@ def test_acp_agent_config_missing_description_raises():
         ACPAgentConfig(command="my-agent")
 
 
-def test_get_acp_agents_returns_empty_by_default():
-    """After clearing, should return empty dict."""
-    load_acp_config_from_dict({})
-    assert get_acp_agents() == {}
-
-
-def test_app_config_reload_without_acp_agents_clears_previous_state(tmp_path, monkeypatch):
+def test_app_config_from_file_with_acp_agents(tmp_path, monkeypatch):
     config_path = tmp_path / "config.yaml"
     extensions_path = tmp_path / "extensions_config.json"
     extensions_path.write_text(json.dumps({"mcpServers": {}, "skills": {}}), encoding="utf-8")
@@ -157,9 +150,9 @@ def test_app_config_reload_without_acp_agents_clears_previous_state(tmp_path, mo
     monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
 
     config_path.write_text(yaml.safe_dump(config_with_acp), encoding="utf-8")
-    AppConfig.from_file(str(config_path))
-    assert set(get_acp_agents()) == {"codex"}
+    app = AppConfig.from_file(str(config_path))
+    assert set(app.acp_agents) == {"codex"}
 
     config_path.write_text(yaml.safe_dump(config_without_acp), encoding="utf-8")
-    AppConfig.from_file(str(config_path))
-    assert get_acp_agents() == {}
+    app = AppConfig.from_file(str(config_path))
+    assert app.acp_agents == {}