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_app_config_reload.py

@@ -1,13 +1,14 @@
 from __future__ import annotations
 
 import json
-import os
 from pathlib import Path
 
+import pytest
 import yaml
 
-from deerflow.config.agents_api_config import get_agents_api_config
-from deerflow.config.app_config import get_app_config, reset_app_config
+from deerflow.config.app_config import AppConfig
+
+pytestmark = pytest.mark.real_from_file
 
 
 def _write_config(path: Path, *, model_name: str, supports_thinking: bool) -> None:
@@ -29,113 +30,66 @@ def _write_config(path: Path, *, model_name: str, supports_thinking: bool) -> No
     )
 
 
-def _write_config_with_agents_api(
-    path: Path,
-    *,
-    model_name: str,
-    supports_thinking: bool,
-    agents_api: dict | None = None,
-) -> None:
-    config = {
-        "sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"},
-        "models": [
-            {
-                "name": model_name,
-                "use": "langchain_openai:ChatOpenAI",
-                "model": "gpt-test",
-                "supports_thinking": supports_thinking,
-            }
-        ],
-    }
-    if agents_api is not None:
-        config["agents_api"] = agents_api
-
-    path.write_text(yaml.safe_dump(config), encoding="utf-8")
-
-
 def _write_extensions_config(path: Path) -> None:
     path.write_text(json.dumps({"mcpServers": {}, "skills": {}}), encoding="utf-8")
 
 
-def test_get_app_config_reloads_when_file_changes(tmp_path, monkeypatch):
+def test_from_file_reads_model_name(tmp_path, monkeypatch):
+    """``AppConfig.from_file`` is the only lifecycle method now; there is no
+    process-global ``init/current``. Each consumer holds its own captured
+    AppConfig instance.
+    """
     config_path = tmp_path / "config.yaml"
     extensions_path = tmp_path / "extensions_config.json"
     _write_extensions_config(extensions_path)
-    _write_config(config_path, model_name="first-model", supports_thinking=False)
+    _write_config(config_path, model_name="test-model", supports_thinking=False)
 
     monkeypatch.setenv("DEER_FLOW_CONFIG_PATH", str(config_path))
     monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
-    reset_app_config()
 
-    try:
-        initial = get_app_config()
-        assert initial.models[0].supports_thinking is False
-
-        _write_config(config_path, model_name="first-model", supports_thinking=True)
-        next_mtime = config_path.stat().st_mtime + 5
-        os.utime(config_path, (next_mtime, next_mtime))
-
-        reloaded = get_app_config()
-        assert reloaded.models[0].supports_thinking is True
-        assert reloaded is not initial
-    finally:
-        reset_app_config()
+    config = AppConfig.from_file(str(config_path))
+    assert config.models[0].name == "test-model"
 
 
-def test_get_app_config_reloads_when_config_path_changes(tmp_path, monkeypatch):
-    config_a = tmp_path / "config-a.yaml"
-    config_b = tmp_path / "config-b.yaml"
-    extensions_path = tmp_path / "extensions_config.json"
-    _write_extensions_config(extensions_path)
-    _write_config(config_a, model_name="model-a", supports_thinking=False)
-    _write_config(config_b, model_name="model-b", supports_thinking=True)
-
-    monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
-    monkeypatch.setenv("DEER_FLOW_CONFIG_PATH", str(config_a))
-    reset_app_config()
-
-    try:
-        first = get_app_config()
-        assert first.models[0].name == "model-a"
-
-        monkeypatch.setenv("DEER_FLOW_CONFIG_PATH", str(config_b))
-        second = get_app_config()
-        assert second.models[0].name == "model-b"
-        assert second is not first
-    finally:
-        reset_app_config()
-
-
-def test_get_app_config_resets_agents_api_config_when_section_removed(tmp_path, monkeypatch):
+def test_from_file_each_call_returns_fresh_instance(tmp_path, monkeypatch):
+    """Two reads of the same file produce separate AppConfig instances —
+    no hidden singleton, no memoization. Callers decide when to re-read.
+    """
     config_path = tmp_path / "config.yaml"
     extensions_path = tmp_path / "extensions_config.json"
     _write_extensions_config(extensions_path)
-    _write_config_with_agents_api(
-        config_path,
-        model_name="first-model",
-        supports_thinking=False,
-        agents_api={"enabled": True},
+    _write_config(config_path, model_name="model-a", supports_thinking=False)
+
+    monkeypatch.setenv("DEER_FLOW_CONFIG_PATH", str(config_path))
+    monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
+
+    config_a = AppConfig.from_file(str(config_path))
+    assert config_a.models[0].name == "model-a"
+
+    _write_config(config_path, model_name="model-b", supports_thinking=True)
+    config_b = AppConfig.from_file(str(config_path))
+    assert config_b.models[0].name == "model-b"
+    assert config_a is not config_b
+
+
+def test_config_version_check(tmp_path, monkeypatch):
+    config_path = tmp_path / "config.yaml"
+    extensions_path = tmp_path / "extensions_config.json"
+    _write_extensions_config(extensions_path)
+
+    config_path.write_text(
+        yaml.safe_dump(
+            {
+                "config_version": 1,
+                "sandbox": {"use": "deerflow.sandbox.local:LocalSandboxProvider"},
+                "models": [],
+            }
+        ),
+        encoding="utf-8",
     )
 
     monkeypatch.setenv("DEER_FLOW_CONFIG_PATH", str(config_path))
     monkeypatch.setenv("DEER_FLOW_EXTENSIONS_CONFIG_PATH", str(extensions_path))
-    reset_app_config()
 
-    try:
-        initial = get_app_config()
-        assert initial.models[0].name == "first-model"
-        assert get_agents_api_config().enabled is True
-
-        _write_config_with_agents_api(
-            config_path,
-            model_name="first-model",
-            supports_thinking=False,
-        )
-        next_mtime = config_path.stat().st_mtime + 5
-        os.utime(config_path, (next_mtime, next_mtime))
-
-        reloaded = get_app_config()
-        assert reloaded is not initial
-        assert get_agents_api_config().enabled is False
-    finally:
-        reset_app_config()
+    config = AppConfig.from_file(str(config_path))
+    assert config is not None