Rename owner_id to user_id across all persistence models, repositories,
stores, routers, and tests for clearer semantics. Rename thread_meta_repo
to thread_store for consistency with run_store/run_event_store naming.
Add ThreadMetaStore return type annotation to get_thread_store().
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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>