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/app/gateway/deps.py

@@ -46,15 +46,15 @@ async def langgraph_runtime(app: FastAPI) -> AsyncGenerator[None, None]:
         # Initialize repositories — one get_session_factory() call for all.
         sf = get_session_factory()
         if sf is not None:
-            from deerflow.persistence.repositories.feedback_repo import FeedbackRepository
-            from deerflow.persistence.repositories.run_repo import RunRepository
-            from deerflow.persistence.repositories.thread_meta_repo import ThreadMetaRepository
+            from deerflow.persistence.feedback import FeedbackRepository
+            from deerflow.persistence.run import RunRepository
+            from deerflow.persistence.thread_meta import ThreadMetaRepository
 
             app.state.run_store = RunRepository(sf)
             app.state.feedback_repo = FeedbackRepository(sf)
             app.state.thread_meta_repo = ThreadMetaRepository(sf)
         else:
-            from deerflow.persistence.repositories.thread_meta_memory import MemoryThreadMetaStore
+            from deerflow.persistence.thread_meta import MemoryThreadMetaStore
             from deerflow.runtime.runs.store.memory import MemoryRunStore
 
             app.state.run_store = MemoryRunStore()

backend/packages/harness/deerflow/persistence/feedback/__init__.py

@@ -0,0 +1,6 @@
+"""Feedback persistence — ORM and SQL repository."""
+
+from deerflow.persistence.feedback.model import FeedbackRow
+from deerflow.persistence.feedback.sql import FeedbackRepository
+
+__all__ = ["FeedbackRepository", "FeedbackRow"]

backend/packages/harness/deerflow/persistence/feedback/sql.py

@@ -11,7 +11,7 @@ from datetime import UTC, datetime
 from sqlalchemy import case, func, select
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
-from deerflow.persistence.models.feedback import FeedbackRow
+from deerflow.persistence.feedback.model import FeedbackRow
 
 
 class FeedbackRepository:

backend/packages/harness/deerflow/persistence/models/__init__.py

@@ -1,6 +1,21 @@
-from deerflow.persistence.models.feedback import FeedbackRow
-from deerflow.persistence.models.run import RunRow
+"""ORM model registration entry point.
+
+Importing this module ensures all ORM models are registered with
+``Base.metadata`` so Alembic autogenerate detects every table.
+
+The actual ORM classes have moved to entity-specific subpackages:
+- ``deerflow.persistence.thread_meta``
+- ``deerflow.persistence.run``
+- ``deerflow.persistence.feedback``
+
+``RunEventRow`` remains in ``deerflow.persistence.models.run_event`` because
+its storage implementation lives in ``deerflow.runtime.events.store.db`` and
+there is no matching entity directory.
+"""
+
+from deerflow.persistence.feedback.model import FeedbackRow
 from deerflow.persistence.models.run_event import RunEventRow
-from deerflow.persistence.models.thread_meta import ThreadMetaRow
+from deerflow.persistence.run.model import RunRow
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
 
 __all__ = ["FeedbackRow", "RunEventRow", "RunRow", "ThreadMetaRow"]

backend/packages/harness/deerflow/persistence/repositories/__init__.py

@@ -1,5 +0,0 @@
-from deerflow.persistence.repositories.feedback_repo import FeedbackRepository
-from deerflow.persistence.repositories.run_repo import RunRepository
-from deerflow.persistence.repositories.thread_meta_repo import ThreadMetaRepository
-
-__all__ = ["FeedbackRepository", "RunRepository", "ThreadMetaRepository"]

backend/packages/harness/deerflow/persistence/run/__init__.py

@@ -0,0 +1,6 @@
+"""Run metadata persistence — ORM and SQL repository."""
+
+from deerflow.persistence.run.model import RunRow
+from deerflow.persistence.run.sql import RunRepository
+
+__all__ = ["RunRepository", "RunRow"]

backend/packages/harness/deerflow/persistence/run/sql.py

@@ -14,7 +14,7 @@ from typing import Any
 from sqlalchemy import func, select, update
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
-from deerflow.persistence.models.run import RunRow
+from deerflow.persistence.run.model import RunRow
 from deerflow.runtime.runs.store.base import RunStore
 
 

backend/packages/harness/deerflow/persistence/thread_meta/__init__.py

@@ -0,0 +1,13 @@
+"""Thread metadata persistence — ORM, abstract store, and concrete implementations."""
+
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.persistence.thread_meta.memory import MemoryThreadMetaStore
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
+from deerflow.persistence.thread_meta.sql import ThreadMetaRepository
+
+__all__ = [
+    "MemoryThreadMetaStore",
+    "ThreadMetaRepository",
+    "ThreadMetaRow",
+    "ThreadMetaStore",
+]

backend/packages/harness/deerflow/persistence/thread_meta/memory.py

@@ -12,7 +12,7 @@ from typing import Any
 
 from langgraph.store.base import BaseStore
 
-from deerflow.persistence.repositories.thread_meta_base import ThreadMetaStore
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
 
 THREADS_NS: tuple[str, ...] = ("threads",)
 

backend/packages/harness/deerflow/persistence/thread_meta/sql.py

@@ -8,8 +8,8 @@ from typing import Any
 from sqlalchemy import select, update
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
-from deerflow.persistence.models.thread_meta import ThreadMetaRow
-from deerflow.persistence.repositories.thread_meta_base import ThreadMetaStore
+from deerflow.persistence.thread_meta.base import ThreadMetaStore
+from deerflow.persistence.thread_meta.model import ThreadMetaRow
 
 
 class ThreadMetaRepository(ThreadMetaStore):

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):