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/packages/harness/deerflow/runtime/store/async_provider.py

@@ -23,7 +23,7 @@ from collections.abc import AsyncIterator
 
 from langgraph.store.base import BaseStore
 
-from deerflow.config.app_config import get_app_config
+from deerflow.config.app_config import AppConfig
 from deerflow.runtime.store.provider import POSTGRES_CONN_REQUIRED, POSTGRES_STORE_INSTALL, SQLITE_STORE_INSTALL, ensure_sqlite_parent_dir, resolve_sqlite_conn_str
 
 logger = logging.getLogger(__name__)
@@ -86,28 +86,26 @@ async def _async_store(config) -> AsyncIterator[BaseStore]:
 
 
 @contextlib.asynccontextmanager
-async def make_store() -> AsyncIterator[BaseStore]:
+async def make_store(app_config: AppConfig) -> AsyncIterator[BaseStore]:
     """Async context manager that yields a Store whose backend matches the
     configured checkpointer.
 
     Reads from the same ``checkpointer`` section of *config.yaml* used by
-    :func:`deerflow.agents.checkpointer.async_provider.make_checkpointer` so
+    :func:`deerflow.runtime.checkpointer.async_provider.make_checkpointer` so
     that both singletons always use the same persistence technology::
 
-        async with make_store() as store:
+        async with make_store(app_config) as store:
             app.state.store = store
 
     Yields an :class:`~langgraph.store.memory.InMemoryStore` when no
     ``checkpointer`` section is configured (emits a WARNING in that case).
     """
-    config = get_app_config()
-
-    if config.checkpointer is None:
+    if app_config.checkpointer is None:
         from langgraph.store.memory import InMemoryStore
 
         logger.warning("No 'checkpointer' section in config.yaml — using InMemoryStore for the store. Thread list will be lost on server restart. Configure a sqlite or postgres backend for persistence.")
         yield InMemoryStore()
         return
 
-    async with _async_store(config.checkpointer) as store:
+    async with _async_store(app_config.checkpointer) as store:
         yield store

backend/packages/harness/deerflow/runtime/store/provider.py

@@ -26,7 +26,7 @@ from collections.abc import Iterator
 
 from langgraph.store.base import BaseStore
 
-from deerflow.config.app_config import get_app_config
+from deerflow.config.app_config import AppConfig
 from deerflow.runtime.store._sqlite_utils import ensure_sqlite_parent_dir, resolve_sqlite_conn_str
 
 logger = logging.getLogger(__name__)
@@ -100,7 +100,7 @@ _store: BaseStore | None = None
 _store_ctx = None  # open context manager keeping the connection alive
 
 
-def get_store() -> BaseStore:
+def get_store(app_config: AppConfig) -> BaseStore:
     """Return the global sync Store singleton, creating it on first call.
 
     Returns an :class:`~langgraph.store.memory.InMemoryStore` when no
@@ -115,19 +115,10 @@ def get_store() -> BaseStore:
     if _store is not None:
         return _store
 
-    # Lazily load app config, mirroring the checkpointer singleton pattern so
-    # that tests that set the global checkpointer config explicitly remain isolated.
-    from deerflow.config.app_config import _app_config
-    from deerflow.config.checkpointer_config import get_checkpointer_config
-
-    config = get_checkpointer_config()
-
-    if config is None and _app_config is None:
-        try:
-            get_app_config()
-        except FileNotFoundError:
-            pass
-        config = get_checkpointer_config()
+    # See matching comment in checkpointer/provider.py: a missing config.yaml
+    # is a deployment error, not a cue to silently pick InMemoryStore. Only
+    # the explicit "no checkpointer section" path falls through to memory.
+    config = app_config.checkpointer
 
     if config is None:
         from langgraph.store.memory import InMemoryStore
@@ -163,26 +154,25 @@ def reset_store() -> None:
 
 
 @contextlib.contextmanager
-def store_context() -> Iterator[BaseStore]:
+def store_context(app_config: AppConfig) -> Iterator[BaseStore]:
     """Sync context manager that yields a Store and cleans up on exit.
 
     Unlike :func:`get_store`, this does **not** cache the instance — each
     ``with`` block creates and destroys its own connection.  Use it in CLI
     scripts or tests where you want deterministic cleanup::
 
-        with store_context() as store:
+        with store_context(app_config) as store:
             store.put(("threads",), thread_id, {...})
 
     Yields an :class:`~langgraph.store.memory.InMemoryStore` when no
     checkpointer is configured in *config.yaml*.
     """
-    config = get_app_config()
-    if config.checkpointer is None:
+    if app_config.checkpointer is None:
         from langgraph.store.memory import InMemoryStore
 
         logger.warning("No 'checkpointer' section in config.yaml — using InMemoryStore for the store. Thread list will be lost on server restart. Configure a sqlite or postgres backend for persistence.")
         yield InMemoryStore()
         return
 
-    with _sync_store_cm(config.checkpointer) as store:
+    with _sync_store_cm(app_config.checkpointer) as store:
         yield store