test+config: comprehensive Phase 2 test coverage + deprecate checkpointer config

- config.example.yaml: deprecate standalone checkpointer section, activate
  unified database:sqlite as default (drives both checkpointer + app data)
- New: test_thread_meta_repo.py (14 tests) — full ThreadMetaRepository coverage
  including check_access owner logic, list_by_owner pagination
- Extended test_run_repository.py (+4 tests) — completion preserves fields,
  list ordering desc, limit, owner_none returns all
- Extended test_run_journal.py (+8 tests) — on_chain_error, track_tokens=false,
  middleware no ai_message, unknown caller tokens, convenience fields,
  tool_error, non-summarization custom event
- Extended test_run_event_store.py (+7 tests) — DB batch seq continuity,
  make_run_event_store factory (memory/db/jsonl/fallback/unknown)
- Extended test_phase2b_integration.py (+4 tests) — create_or_reject persists,
  follow-up metadata, summarization in history, full DB-backed lifecycle
- Fixed DB integration test to use proper fake objects (not MagicMock)
  for JSON-serializable metadata
- 157 total Phase 2 tests pass, zero regressions

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

backend/tests/test_run_event_store.py

@@ -357,6 +357,102 @@ class TestDbRunEventStore:
 
         await close_engine()
 
+    @pytest.mark.anyio
+    async def test_put_batch_seq_continuity(self, tmp_path):
+        """Batch write produces continuous seq values with no gaps."""
+        from deerflow.persistence.engine import close_engine, get_session_factory, init_engine
+        from deerflow.runtime.events.store.db import DbRunEventStore
+
+        url = f"sqlite+aiosqlite:///{tmp_path / 'test.db'}"
+        await init_engine("sqlite", url=url, sqlite_dir=str(tmp_path))
+        s = DbRunEventStore(get_session_factory())
+
+        events = [{"thread_id": "t1", "run_id": "r1", "event_type": "trace", "category": "trace"} for _ in range(50)]
+        results = await s.put_batch(events)
+        seqs = [r["seq"] for r in results]
+        assert seqs == list(range(1, 51))
+        await close_engine()
+
+
+# -- Factory tests --
+
+
+class TestMakeRunEventStore:
+    """Tests for the make_run_event_store factory function."""
+
+    @pytest.mark.anyio
+    async def test_memory_backend_default(self):
+        from deerflow.runtime.events.store import make_run_event_store
+
+        store = make_run_event_store(None)
+        assert type(store).__name__ == "MemoryRunEventStore"
+
+    @pytest.mark.anyio
+    async def test_memory_backend_explicit(self):
+        from unittest.mock import MagicMock
+
+        from deerflow.runtime.events.store import make_run_event_store
+
+        config = MagicMock()
+        config.backend = "memory"
+        store = make_run_event_store(config)
+        assert type(store).__name__ == "MemoryRunEventStore"
+
+    @pytest.mark.anyio
+    async def test_db_backend_with_engine(self, tmp_path):
+        from unittest.mock import MagicMock
+
+        from deerflow.persistence.engine import close_engine, init_engine
+        from deerflow.runtime.events.store import make_run_event_store
+
+        url = f"sqlite+aiosqlite:///{tmp_path / 'test.db'}"
+        await init_engine("sqlite", url=url, sqlite_dir=str(tmp_path))
+
+        config = MagicMock()
+        config.backend = "db"
+        config.max_trace_content = 10240
+        store = make_run_event_store(config)
+        assert type(store).__name__ == "DbRunEventStore"
+        await close_engine()
+
+    @pytest.mark.anyio
+    async def test_db_backend_no_engine_falls_back(self):
+        """db backend without engine falls back to memory."""
+        from unittest.mock import MagicMock
+
+        from deerflow.persistence.engine import close_engine, init_engine
+        from deerflow.runtime.events.store import make_run_event_store
+
+        await init_engine("memory")  # no engine created
+
+        config = MagicMock()
+        config.backend = "db"
+        store = make_run_event_store(config)
+        assert type(store).__name__ == "MemoryRunEventStore"
+        await close_engine()
+
+    @pytest.mark.anyio
+    async def test_jsonl_backend(self):
+        from unittest.mock import MagicMock
+
+        from deerflow.runtime.events.store import make_run_event_store
+
+        config = MagicMock()
+        config.backend = "jsonl"
+        store = make_run_event_store(config)
+        assert type(store).__name__ == "JsonlRunEventStore"
+
+    @pytest.mark.anyio
+    async def test_unknown_backend_raises(self):
+        from unittest.mock import MagicMock
+
+        from deerflow.runtime.events.store import make_run_event_store
+
+        config = MagicMock()
+        config.backend = "redis"
+        with pytest.raises(ValueError, match="Unknown"):
+            make_run_event_store(config)
+
 
 # -- JSONL-specific tests --