refactor(persistence): organize entities into per-entity directories

Restructure the persistence layer from horizontal "models/ + repositories/"
split into vertical entity-aligned directories. Each entity (thread_meta,
run, feedback) now owns its ORM model, abstract interface (where applicable),
and concrete implementations under a single directory with an aggregating
__init__.py for one-line imports.

Layout:
  persistence/thread_meta/{base,model,sql,memory}.py
  persistence/run/{model,sql}.py
  persistence/feedback/{model,sql}.py

models/__init__.py is kept as a facade so Alembic autogenerate continues to
discover all ORM tables via Base.metadata. RunEventRow remains under
models/run_event.py because its storage implementation lives in
runtime/events/store/db.py and has no matching repository directory.

The repositories/ directory is removed entirely. All call sites in
gateway/deps.py and tests are updated to import from the new entity
packages, e.g.:

    from deerflow.persistence.thread_meta import ThreadMetaRepository
    from deerflow.persistence.run import RunRepository
    from deerflow.persistence.feedback import FeedbackRepository

Full test suite passes (1690 passed, 14 skipped).

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

backend/tests/test_feedback.py

@@ -5,7 +5,7 @@ Uses temp SQLite DB for ORM tests.
 
 import pytest
 
-from deerflow.persistence.repositories.feedback_repo import FeedbackRepository
+from deerflow.persistence.feedback import FeedbackRepository
 
 
 async def _make_feedback_repo(tmp_path):

backend/tests/test_run_journal.py

@@ -373,7 +373,7 @@ class TestDbBackedLifecycle:
     async def test_full_lifecycle_with_sqlite(self, tmp_path):
         """Full lifecycle with SQLite-backed RunRepository + DbRunEventStore."""
         from deerflow.persistence.engine import close_engine, get_session_factory, init_engine
-        from deerflow.persistence.repositories.run_repo import RunRepository
+        from deerflow.persistence.run import RunRepository
         from deerflow.runtime.events.store.db import DbRunEventStore
         from deerflow.runtime.runs.manager import RunManager
 

backend/tests/test_run_repository.py

@@ -5,7 +5,7 @@ Uses a temp SQLite DB to test ORM-backed CRUD operations.
 
 import pytest
 
-from deerflow.persistence.repositories.run_repo import RunRepository
+from deerflow.persistence.run import RunRepository
 
 
 async def _make_repo(tmp_path):

backend/tests/test_thread_meta_repo.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from deerflow.persistence.repositories.thread_meta_repo import ThreadMetaRepository
+from deerflow.persistence.thread_meta import ThreadMetaRepository
 
 
 async def _make_repo(tmp_path):