feat(persistence): add SQLAlchemy 2.0 async ORM scaffold

Introduce a unified database configuration (DatabaseConfig) that
controls both the LangGraph checkpointer and the DeerFlow application
persistence layer from a single `database:` config section.

New modules:
- deerflow.config.database_config — Pydantic config with memory/sqlite/postgres backends
- deerflow.persistence — async engine lifecycle, DeclarativeBase with to_dict mixin, Alembic skeleton
- deerflow.runtime.runs.store — RunStore ABC + MemoryRunStore implementation

Gateway integration initializes/tears down the persistence engine in
the existing langgraph_runtime() context manager. Legacy checkpointer
config is preserved for backward compatibility.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

backend/app/gateway/deps.py

@@ -14,6 +14,7 @@ from contextlib import AsyncExitStack, asynccontextmanager
 from fastapi import FastAPI, HTTPException, Request
 
 from deerflow.runtime import RunManager, StreamBridge
+from deerflow.runtime.runs.store.base import RunStore
 
 
 @asynccontextmanager
@@ -26,18 +27,33 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
             yield
     """
     from deerflow.agents.checkpointer.async_provider import make_checkpointer
+    from deerflow.config import get_app_config
+    from deerflow.persistence.engine import close_engine, init_engine_from_config
     from deerflow.runtime import make_store, make_stream_bridge
+    from deerflow.runtime.runs.store.memory import MemoryRunStore
 
     async with AsyncExitStack() as stack:
         app.state.stream_bridge = await stack.enter_async_context(make_stream_bridge())
         app.state.checkpointer = await stack.enter_async_context(make_checkpointer())
         app.state.store = await stack.enter_async_context(make_store())
         app.state.run_manager = RunManager()
-        yield
+
+        # Initialize persistence layer from unified database config
+        config = get_app_config()
+        await init_engine_from_config(config.database)
+
+        # Initialize run store (MemoryRunStore for now; switch to ORM-backed
+        # RunRepository when models are implemented)
+        app.state.run_store = MemoryRunStore()
+
+        try:
+            yield
+        finally:
+            await close_engine()
 
 
 # ---------------------------------------------------------------------------
-# Getters – called by routers per-request
+# Getters -- called by routers per-request
 # ---------------------------------------------------------------------------
 
 
@@ -68,3 +84,20 @@ def get_checkpointer(request: Request):
 def get_store(request: Request):
     """Return the global store (may be ``None`` if not configured)."""
     return getattr(request.app.state, "store", None)
+
+
+def get_run_store(request: Request) -> RunStore:
+    """Return the RunStore, or 503 if not available."""
+    store = getattr(request.app.state, "run_store", None)
+    if store is None:
+        raise HTTPException(status_code=503, detail="Run store not available")
+    return store
+
+
+async def get_current_user(request: Request) -> str | None:
+    """Extract user identity from request.
+
+    Phase 2: always returns None (no authentication).
+    Phase 3: extract user_id from JWT / session / API key header.
+    """
+    return None