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/tests/test_checkpointer.py

@@ -6,7 +6,7 @@ from unittest.mock import AsyncMock, MagicMock, patch
 import pytest
 
 import deerflow.config.app_config as app_config_module
-from deerflow.agents.checkpointer import get_checkpointer, reset_checkpointer
+from deerflow.runtime.checkpointer import get_checkpointer, reset_checkpointer
 from deerflow.config.checkpointer_config import (
     CheckpointerConfig,
     get_checkpointer_config,
@@ -78,7 +78,7 @@ class TestGetCheckpointer:
         """get_checkpointer should return InMemorySaver when not configured."""
         from langgraph.checkpoint.memory import InMemorySaver
 
-        with patch("deerflow.agents.checkpointer.provider.get_app_config", side_effect=FileNotFoundError):
+        with patch("deerflow.runtime.checkpointer.provider.get_app_config", side_effect=FileNotFoundError):
             cp = get_checkpointer()
         assert cp is not None
         assert isinstance(cp, InMemorySaver)

backend/tests/test_checkpointer_none_fix.py

@@ -12,14 +12,14 @@ class TestCheckpointerNoneFix:
     @pytest.mark.anyio
     async def test_async_make_checkpointer_returns_in_memory_saver_when_not_configured(self):
         """make_checkpointer should return InMemorySaver when config.checkpointer is None."""
-        from deerflow.agents.checkpointer.async_provider import make_checkpointer
+        from deerflow.runtime.checkpointer.async_provider import make_checkpointer
 
         # Mock get_app_config to return a config with checkpointer=None and database=None
         mock_config = MagicMock()
         mock_config.checkpointer = None
         mock_config.database = None
 
-        with patch("deerflow.agents.checkpointer.async_provider.get_app_config", return_value=mock_config):
+        with patch("deerflow.runtime.checkpointer.async_provider.get_app_config", return_value=mock_config):
             async with make_checkpointer() as checkpointer:
                 # Should return InMemorySaver, not None
                 assert checkpointer is not None
@@ -36,13 +36,13 @@ class TestCheckpointerNoneFix:
 
     def test_sync_checkpointer_context_returns_in_memory_saver_when_not_configured(self):
         """checkpointer_context should return InMemorySaver when config.checkpointer is None."""
-        from deerflow.agents.checkpointer.provider import checkpointer_context
+        from deerflow.runtime.checkpointer.provider import checkpointer_context
 
         # Mock get_app_config to return a config with checkpointer=None
         mock_config = MagicMock()
         mock_config.checkpointer = None
 
-        with patch("deerflow.agents.checkpointer.provider.get_app_config", return_value=mock_config):
+        with patch("deerflow.runtime.checkpointer.provider.get_app_config", return_value=mock_config):
             with checkpointer_context() as checkpointer:
                 # Should return InMemorySaver, not None
                 assert checkpointer is not None

backend/tests/test_client.py

@@ -817,7 +817,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]) as mock_build_middlewares,
             patch("deerflow.client.apply_prompt_template", return_value="prompt") as mock_apply_prompt,
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._agent_name = "custom-agent"
             client._available_skills = {"test_skill"}
@@ -842,7 +842,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=mock_checkpointer),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=mock_checkpointer),
         ):
             client._ensure_agent(config)
 
@@ -867,7 +867,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", side_effect=fake_build_middlewares),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
 
@@ -886,7 +886,7 @@ class TestEnsureAgent:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=None),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=None),
         ):
             client._ensure_agent(config)
 
@@ -1844,7 +1844,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config_a)
             first_agent = client._agent
@@ -1872,7 +1872,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
             client._ensure_agent(config)
@@ -1897,7 +1897,7 @@ class TestScenarioAgentRecreation:
             patch("deerflow.client._build_middlewares", return_value=[]),
             patch("deerflow.client.apply_prompt_template", return_value="prompt"),
             patch.object(client, "_get_tools", return_value=[]),
-            patch("deerflow.agents.checkpointer.get_checkpointer", return_value=MagicMock()),
+            patch("deerflow.runtime.checkpointer.get_checkpointer", return_value=MagicMock()),
         ):
             client._ensure_agent(config)
             client.reset_agent()

backend/tests/test_persistence_scaffold.py

@@ -24,18 +24,19 @@ class TestDatabaseConfig:
         assert c.backend == "memory"
         assert c.pool_size == 5
 
-    def test_sqlite_paths_are_different(self):
+    def test_sqlite_paths_unified(self):
         c = DatabaseConfig(backend="sqlite", sqlite_dir="./mydata")
-        assert c.checkpointer_sqlite_path.endswith("checkpoints.db")
-        assert c.app_sqlite_path.endswith("app.db")
-        assert "mydata" in c.checkpointer_sqlite_path
-        assert c.checkpointer_sqlite_path != c.app_sqlite_path
+        assert c.sqlite_path.endswith("deerflow.db")
+        assert "mydata" in c.sqlite_path
+        # Backward-compatible aliases point to the same file
+        assert c.checkpointer_sqlite_path == c.sqlite_path
+        assert c.app_sqlite_path == c.sqlite_path
 
     def test_app_sqlalchemy_url_sqlite(self):
         c = DatabaseConfig(backend="sqlite", sqlite_dir="./data")
         url = c.app_sqlalchemy_url
         assert url.startswith("sqlite+aiosqlite:///")
-        assert "app.db" in url
+        assert "deerflow.db" in url
 
     def test_app_sqlalchemy_url_postgres(self):
         c = DatabaseConfig(