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_uploads_router.py

@@ -4,6 +4,7 @@ from io import BytesIO
 from pathlib import Path
 from unittest.mock import AsyncMock, MagicMock, patch
 
+from _router_auth_helpers import call_unwrapped
 from fastapi import UploadFile
 
 from app.gateway.routers import uploads
@@ -25,7 +26,7 @@ def test_upload_files_writes_thread_storage_and_skips_local_sandbox_sync(tmp_pat
         patch.object(uploads, "get_sandbox_provider", return_value=provider),
     ):
         file = UploadFile(filename="notes.txt", file=BytesIO(b"hello uploads"))
-        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=[file]))
 
     assert result.success is True
     assert len(result.files) == 1
@@ -107,7 +108,7 @@ def test_upload_files_syncs_non_local_sandbox_and_marks_markdown_file(tmp_path):
         patch.object(uploads, "convert_file_to_markdown", AsyncMock(side_effect=fake_convert)),
     ):
         file = UploadFile(filename="report.pdf", file=BytesIO(b"pdf-bytes"))
-        result = asyncio.run(uploads.upload_files("thread-aio", files=[file]))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=[file]))
 
     assert result.success is True
     assert len(result.files) == 1
@@ -146,7 +147,7 @@ def test_upload_files_makes_non_local_files_sandbox_writable(tmp_path):
         patch.object(uploads, "_make_file_sandbox_writable") as make_writable,
     ):
         file = UploadFile(filename="report.pdf", file=BytesIO(b"pdf-bytes"))
-        result = asyncio.run(uploads.upload_files("thread-aio", files=[file]))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-aio", request=MagicMock(), files=[file]))
 
     assert result.success is True
     make_writable.assert_any_call(thread_uploads_dir / "report.pdf")
@@ -170,7 +171,7 @@ def test_upload_files_does_not_adjust_permissions_for_local_sandbox(tmp_path):
         patch.object(uploads, "_make_file_sandbox_writable") as make_writable,
     ):
         file = UploadFile(filename="notes.txt", file=BytesIO(b"hello uploads"))
-        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=[file]))
 
     assert result.success is True
     make_writable.assert_not_called()
@@ -221,13 +222,13 @@ def test_upload_files_rejects_dotdot_and_dot_filenames(tmp_path):
         # These filenames must be rejected outright
         for bad_name in ["..", "."]:
             file = UploadFile(filename=bad_name, file=BytesIO(b"data"))
-            result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+            result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=[file]))
             assert result.success is True
             assert result.files == [], f"Expected no files for unsafe filename {bad_name!r}"
 
         # Path-traversal prefixes are stripped to the basename and accepted safely
         file = UploadFile(filename="../etc/passwd", file=BytesIO(b"data"))
-        result = asyncio.run(uploads.upload_files("thread-local", files=[file]))
+        result = asyncio.run(call_unwrapped(uploads.upload_files, "thread-local", request=MagicMock(), files=[file]))
         assert result.success is True
         assert len(result.files) == 1
         assert result.files[0]["filename"] == "passwd"
@@ -243,7 +244,7 @@ def test_delete_uploaded_file_removes_generated_markdown_companion(tmp_path):
     (thread_uploads_dir / "report.md").write_text("converted", encoding="utf-8")
 
     with patch.object(uploads, "get_uploads_dir", return_value=thread_uploads_dir):
-        result = asyncio.run(uploads.delete_uploaded_file("thread-aio", "report.pdf"))
+        result = asyncio.run(call_unwrapped(uploads.delete_uploaded_file, "thread-aio", "report.pdf", request=MagicMock()))
 
     assert result == {"success": True, "message": "Deleted report.pdf"}
     assert not (thread_uploads_dir / "report.pdf").exists()