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/app/channels/feishu.py

@@ -13,6 +13,7 @@ from app.channels.base import Channel
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 
 logger = logging.getLogger(__name__)
@@ -344,8 +345,9 @@ class FeishuChannel(Channel):
             return f"Failed to obtain the [{type}]"
 
         paths = get_paths()
-        paths.ensure_thread_dirs(thread_id)
-        uploads_dir = paths.sandbox_uploads_dir(thread_id).resolve()
+        user_id = get_effective_user_id()
+        paths.ensure_thread_dirs(thread_id, user_id=user_id)
+        uploads_dir = paths.sandbox_uploads_dir(thread_id, user_id=user_id).resolve()
 
         ext = "png" if type == "image" else "bin"
         raw_filename = getattr(response, "file_name", "") or f"feishu_{file_key[-12:]}.{ext}"
@@ -373,7 +375,9 @@ class FeishuChannel(Channel):
         virtual_path = f"{VIRTUAL_PATH_PREFIX}/uploads/{resolved_target.name}"
 
         try:
-            sandbox_provider = get_sandbox_provider()
+            from deerflow.config.app_config import AppConfig
+
+            sandbox_provider = get_sandbox_provider(AppConfig.from_file())
             sandbox_id = sandbox_provider.acquire(thread_id)
             if sandbox_id != "local":
                 sandbox = sandbox_provider.get(sandbox_id)

backend/app/channels/manager.py

@@ -17,6 +17,7 @@ from langgraph_sdk.errors import ConflictError
 from app.channels.commands import KNOWN_CHANNEL_COMMANDS
 from app.channels.message_bus import InboundMessage, InboundMessageType, MessageBus, OutboundMessage, ResolvedAttachment
 from app.channels.store import ChannelStore
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -342,14 +343,15 @@ def _resolve_attachments(thread_id: str, artifacts: list[str]) -> list[ResolvedA
 
     attachments: list[ResolvedAttachment] = []
     paths = get_paths()
-    outputs_dir = paths.sandbox_outputs_dir(thread_id).resolve()
+    user_id = get_effective_user_id()
+    outputs_dir = paths.sandbox_outputs_dir(thread_id, user_id=user_id).resolve()
     for virtual_path in artifacts:
         # Security: only allow files from the agent outputs directory
         if not virtual_path.startswith(_OUTPUTS_VIRTUAL_PREFIX):
             logger.warning("[Manager] rejected non-outputs artifact path: %s", virtual_path)
             continue
         try:
-            actual = paths.resolve_virtual_path(thread_id, virtual_path)
+            actual = paths.resolve_virtual_path(thread_id, virtual_path, user_id=user_id)
             # Verify the resolved path is actually under the outputs directory
             # (guards against path-traversal even after prefix check)
             try:

backend/app/channels/service.py

@@ -4,13 +4,16 @@ from __future__ import annotations
 
 import logging
 import os
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from app.channels.base import Channel
 from app.channels.manager import DEFAULT_GATEWAY_URL, DEFAULT_LANGGRAPH_URL, ChannelManager
 from app.channels.message_bus import MessageBus
 from app.channels.store import ChannelStore
 
+if TYPE_CHECKING:
+    from deerflow.config.app_config import AppConfig
+
 logger = logging.getLogger(__name__)
 
 # Channel name → import path for lazy loading
@@ -75,14 +78,11 @@ class ChannelService:
         self._running = False
 
     @classmethod
-    def from_app_config(cls) -> ChannelService:
-        """Create a ChannelService from the application config."""
-        from deerflow.config.app_config import get_app_config
-
-        config = get_app_config()
+    def from_app_config(cls, app_config: AppConfig) -> ChannelService:
+        """Create a ChannelService from an explicit application config."""
         channels_config = {}
         # extra fields are allowed by AppConfig (extra="allow")
-        extra = config.model_extra or {}
+        extra = app_config.model_extra or {}
         if "channels" in extra:
             channels_config = extra["channels"]
         return cls(channels_config=channels_config)
@@ -201,12 +201,12 @@ def get_channel_service() -> ChannelService | None:
     return _channel_service
 
 
-async def start_channel_service() -> ChannelService:
+async def start_channel_service(app_config: AppConfig) -> ChannelService:
     """Create and start the global ChannelService from app config."""
     global _channel_service
     if _channel_service is not None:
         return _channel_service
-    _channel_service = ChannelService.from_app_config()
+    _channel_service = ChannelService.from_app_config(app_config)
     await _channel_service.start()
     return _channel_service