refactor(persistence): unify SQLite to single deerflow.db and move checkpointer to runtime

Merge checkpoints.db and app.db into a single deerflow.db file (WAL mode
handles concurrent access safely). Move checkpointer module from
agents/checkpointer to runtime/checkpointer to better reflect its role
as a runtime infrastructure concern.

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

backend/packages/harness/deerflow/runtime/__init__.py

@@ -5,12 +5,18 @@ Re-exports the public API of :mod:`~deerflow.runtime.runs` and
 directly from ``deerflow.runtime``.
 """
 
+from .checkpointer import checkpointer_context, get_checkpointer, make_checkpointer, reset_checkpointer
 from .runs import ConflictError, DisconnectMode, RunContext, RunManager, RunRecord, RunStatus, UnsupportedStrategyError, run_agent
 from .serialization import serialize, serialize_channel_values, serialize_lc_object, serialize_messages_tuple
 from .store import get_store, make_store, reset_store, store_context
 from .stream_bridge import END_SENTINEL, HEARTBEAT_SENTINEL, MemoryStreamBridge, StreamBridge, StreamEvent, make_stream_bridge
 
 __all__ = [
+    # checkpointer
+    "checkpointer_context",
+    "get_checkpointer",
+    "make_checkpointer",
+    "reset_checkpointer",
     # runs
     "ConflictError",
     "DisconnectMode",