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/packages/harness/deerflow/persistence/migrations/env.py

@@ -0,0 +1,63 @@
+"""Alembic environment for DeerFlow application tables.
+
+ONLY manages DeerFlow's tables (runs, threads_meta, cron_jobs, users).
+LangGraph's checkpointer tables are managed by LangGraph itself -- they
+have their own schema lifecycle and must not be touched by Alembic.
+"""
+
+from __future__ import annotations
+
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy.ext.asyncio import create_async_engine
+
+from deerflow.persistence.base import Base
+
+# Import all models so metadata is populated.
+try:
+    import deerflow.persistence.models  # noqa: F401
+except ImportError:
+    pass
+
+config = context.config
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+target_metadata = Base.metadata
+
+
+def run_migrations_offline() -> None:
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        render_as_batch=True,
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection):
+    context.configure(
+        connection=connection,
+        target_metadata=target_metadata,
+        render_as_batch=True,  # Required for SQLite ALTER TABLE support
+    )
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_migrations_online() -> None:
+    connectable = create_async_engine(config.get_main_option("sqlalchemy.url"))
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+    await connectable.dispose()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    asyncio.run(run_migrations_online())