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/events/store/base.py

@@ -0,0 +1,109 @@
+"""Abstract interface for run event storage.
+
+RunEventStore is the unified storage interface for run event streams.
+Messages (frontend display) and execution traces (debugging/audit) go
+through the same interface, distinguished by the ``category`` field.
+
+Implementations:
+- MemoryRunEventStore: in-memory dict (development, tests)
+- Future: DB-backed store (SQLAlchemy ORM), JSONL file store
+"""
+
+from __future__ import annotations
+
+import abc
+
+
+class RunEventStore(abc.ABC):
+    """Run event stream storage interface.
+
+    All implementations must guarantee:
+    1. put() events are retrievable in subsequent queries
+    2. seq is strictly increasing within the same thread
+    3. list_messages() only returns category="message" events
+    4. list_events() returns all events for the specified run
+    5. Returned dicts match the RunEvent field structure
+    """
+
+    @abc.abstractmethod
+    async def put(
+        self,
+        *,
+        thread_id: str,
+        run_id: str,
+        event_type: str,
+        category: str,
+        content: str | dict = "",
+        metadata: dict | None = None,
+        created_at: str | None = None,
+    ) -> dict:
+        """Write an event, auto-assign seq, return the complete record."""
+
+    @abc.abstractmethod
+    async def put_batch(self, events: list[dict]) -> list[dict]:
+        """Batch-write events. Used by RunJournal flush buffer.
+
+        Each dict's keys match put()'s keyword arguments.
+        Returns complete records with seq assigned.
+        """
+
+    @abc.abstractmethod
+    async def list_messages(
+        self,
+        thread_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+    ) -> list[dict]:
+        """Return displayable messages (category=message) for a thread, ordered by seq ascending.
+
+        Supports bidirectional cursor pagination:
+        - before_seq: return the last ``limit`` records with seq < before_seq (ascending)
+        - after_seq: return the first ``limit`` records with seq > after_seq (ascending)
+        - neither: return the latest ``limit`` records (ascending)
+        """
+
+    @abc.abstractmethod
+    async def list_events(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        event_types: list[str] | None = None,
+        limit: int = 500,
+    ) -> list[dict]:
+        """Return the full event stream for a run, ordered by seq ascending.
+
+        Optionally filter by event_types.
+        """
+
+    @abc.abstractmethod
+    async def list_messages_by_run(
+        self,
+        thread_id: str,
+        run_id: str,
+        *,
+        limit: int = 50,
+        before_seq: int | None = None,
+        after_seq: int | None = None,
+    ) -> list[dict]:
+        """Return displayable messages (category=message) for a specific run, ordered by seq ascending.
+
+        Supports bidirectional cursor pagination:
+        - after_seq: return the first ``limit`` records with seq > after_seq (ascending)
+        - before_seq: return the last ``limit`` records with seq < before_seq (ascending)
+        - neither: return the latest ``limit`` records (ascending)
+        """
+
+    @abc.abstractmethod
+    async def count_messages(self, thread_id: str) -> int:
+        """Count displayable messages (category=message) in a thread."""
+
+    @abc.abstractmethod
+    async def delete_by_thread(self, thread_id: str) -> int:
+        """Delete all events for a thread. Return the number of deleted events."""
+
+    @abc.abstractmethod
+    async def delete_by_run(self, thread_id: str, run_id: str) -> int:
+        """Delete all events for a specific run. Return the number of deleted events."""