Feat: enable sync deleted files for RDBMS & fix remove last file issue (#14615)

### What problem does this PR solve?

Feat: enable sync deleted files for RDBMS & fix remove last file issue

### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)
- [x] New Feature (non-breaking change which adds functionality)

test/unit_test/rag/test_sync_data_source.py

@@ -95,6 +95,18 @@ class _FakeSync(sync_data_source.SyncBase):
         return self._generate_output
 
 
+def _make_fake_doc(doc_id="doc-1", updated_at=None):
+    return types.SimpleNamespace(
+        id=doc_id,
+        semantic_identifier=doc_id,
+        extension=".txt",
+        size_bytes=1,
+        doc_updated_at=updated_at or datetime(2026, 1, 1, tzinfo=timezone.utc),
+        blob=b"x",
+        metadata=None,
+    )
+
+
 def _make_task():
     return {
         "id": "task-1",
@@ -121,19 +133,35 @@ def _patch_common_dependencies(monkeypatch):
 
 @pytest.mark.anyio
 @pytest.mark.p2
-async def test_run_task_logic_skips_cleanup_for_empty_snapshot(monkeypatch):
+async def test_run_task_logic_cleans_up_for_empty_snapshot(monkeypatch):
     cleanup_calls = []
 
     _patch_common_dependencies(monkeypatch)
+
+    def _fake_cleanup(*args, **kwargs):
+        cleanup_calls.append((args, kwargs))
+        return 1, []
+
     monkeypatch.setattr(
         sync_data_source.ConnectorService,
         "cleanup_stale_documents_for_task",
-        lambda *_args, **_kwargs: cleanup_calls.append((_args, _kwargs)),
+        _fake_cleanup,
     )
 
     await _FakeSync((iter(()), []))._run_task_logic(_make_task())
 
-    assert cleanup_calls == []
+    assert cleanup_calls == [
+        (
+            (
+                "task-1",
+                "connector-1",
+                "kb-1",
+                "tenant-1",
+                [],
+            ),
+            {},
+        )
+    ]
 
 
 @pytest.mark.anyio
@@ -170,6 +198,203 @@ async def test_run_task_logic_cleans_up_for_non_empty_snapshot(monkeypatch):
     ]
 
 
+class _FakeRDBMSConnector:
+    instance = None
+
+    def __init__(
+        self,
+        db_type,
+        host,
+        port,
+        database,
+        query,
+        content_columns,
+        metadata_columns=None,
+        id_column=None,
+        timestamp_column=None,
+        batch_size=2,
+    ):
+        self.db_type = db_type
+        self.host = host
+        self.port = port
+        self.database = database
+        self.query = query
+        self.content_columns = content_columns
+        self.metadata_columns = metadata_columns
+        self.id_column = id_column
+        self.timestamp_column = timestamp_column
+        self.batch_size = batch_size
+        self.load_from_state_called = False
+        self.retrieve_all_slim_docs_perm_sync_called = False
+        self.prepare_sync_state_called = False
+        self.load_from_cursor_range_called = False
+        self.persist_sync_state_called = False
+        self._pending_sync_cursor_value = None
+        _FakeRDBMSConnector.instance = self
+
+    def load_credentials(self, credentials):
+        self.credentials = credentials
+
+    def validate_connector_settings(self):
+        return None
+
+    def prepare_sync_state(self, connector_id, config):
+        self.prepare_sync_state_called = True
+        self.prepare_sync_state_args = (connector_id, config)
+
+    def get_saved_sync_cursor_value(self):
+        return None
+
+    def retrieve_all_slim_docs_perm_sync(self, callback=None):
+        del callback
+        self.retrieve_all_slim_docs_perm_sync_called = True
+        yield [types.SimpleNamespace(id="row-1")]
+
+    def load_from_state(self):
+        self.load_from_state_called = True
+        return iter((["full-sync"],))
+
+    def load_from_cursor_range(self, start_value=None, end_value=None):
+        self.load_from_cursor_range_called = True
+        return iter(([ _make_fake_doc("incremental-doc") ],))
+
+    def persist_sync_state(self):
+        self.persist_sync_state_called = True
+
+
+@pytest.mark.anyio
+@pytest.mark.p2
+async def test_rdbms_generate_keeps_deleted_file_snapshot_without_timestamp_column(monkeypatch):
+    monkeypatch.setattr(sync_data_source, "RDBMSConnector", _FakeRDBMSConnector)
+
+    task = {
+        **_make_task(),
+        "reindex": "0",
+        "poll_range_start": datetime(2026, 1, 1, tzinfo=timezone.utc),
+        "skip_connection_log": True,
+    }
+    sync = sync_data_source.MySQL(
+        {
+            "host": "localhost",
+            "port": 3306,
+            "database": "db",
+            "query": "SELECT * FROM t",
+            "content_columns": "name",
+            "credentials": {"username": "u", "password": "p"},
+            "sync_deleted_files": True,
+        }
+    )
+
+    document_generator, file_list = await sync._generate(task)
+    connector = _FakeRDBMSConnector.instance
+
+    assert connector is not None
+    assert connector.load_from_state_called is True
+    assert connector.load_from_cursor_range_called is False
+    assert connector.retrieve_all_slim_docs_perm_sync_called is True
+    assert file_list is not None
+    assert [doc.id for doc in file_list] == ["row-1"]
+    assert list(document_generator) == [["full-sync"]]
+
+
+@pytest.mark.anyio
+@pytest.mark.p2
+async def test_rdbms_cursor_persists_only_after_success(monkeypatch):
+    monkeypatch.setattr(sync_data_source, "RDBMSConnector", _FakeRDBMSConnector)
+    _patch_common_dependencies(monkeypatch)
+    monkeypatch.setattr(
+        sync_data_source.KnowledgebaseService,
+        "get_by_id",
+        lambda *_args, **_kwargs: (True, object()),
+    )
+    monkeypatch.setattr(
+        sync_data_source.SyncLogsService,
+        "increase_docs",
+        lambda *_args, **_kwargs: None,
+    )
+    monkeypatch.setattr(
+        sync_data_source.SyncLogsService,
+        "duplicate_and_parse",
+        lambda *_args, **_kwargs: ([], ["parsed-doc-id"]),
+    )
+
+    task = {
+        **_make_task(),
+        "reindex": "0",
+        "poll_range_start": datetime(2026, 1, 1, tzinfo=timezone.utc),
+        "skip_connection_log": True,
+    }
+    sync = sync_data_source.MySQL(
+        {
+            "host": "localhost",
+            "port": 3306,
+            "database": "db",
+            "query": "SELECT * FROM t",
+            "content_columns": "name",
+            "timestamp_column": "ts",
+            "credentials": {"username": "u", "password": "p"},
+            "sync_deleted_files": False,
+        }
+    )
+
+    await sync._run_task_logic(task)
+
+    connector = _FakeRDBMSConnector.instance
+    assert connector is not None
+    assert connector.persist_sync_state_called is True
+
+
+@pytest.mark.anyio
+@pytest.mark.p2
+async def test_rdbms_cursor_does_not_persist_when_batch_is_skipped(monkeypatch):
+    monkeypatch.setattr(sync_data_source, "RDBMSConnector", _FakeRDBMSConnector)
+    _patch_common_dependencies(monkeypatch)
+    monkeypatch.setattr(
+        sync_data_source.KnowledgebaseService,
+        "get_by_id",
+        lambda *_args, **_kwargs: (True, object()),
+    )
+    monkeypatch.setattr(
+        sync_data_source.SyncLogsService,
+        "increase_docs",
+        lambda *_args, **_kwargs: None,
+    )
+
+    def _raise_in_duplicate_and_parse(*_args, **_kwargs):
+        raise RuntimeError("batch failed")
+
+    monkeypatch.setattr(
+        sync_data_source.SyncLogsService,
+        "duplicate_and_parse",
+        _raise_in_duplicate_and_parse,
+    )
+
+    task = {
+        **_make_task(),
+        "reindex": "0",
+        "poll_range_start": datetime(2026, 1, 1, tzinfo=timezone.utc),
+        "skip_connection_log": True,
+    }
+    sync = sync_data_source.MySQL(
+        {
+            "host": "localhost",
+            "port": 3306,
+            "database": "db",
+            "query": "SELECT * FROM t",
+            "content_columns": "name",
+            "timestamp_column": "ts",
+            "credentials": {"username": "u", "password": "p"},
+            "sync_deleted_files": False,
+        }
+    )
+
+    await sync._run_task_logic(task)
+
+    connector = _FakeRDBMSConnector.instance
+    assert connector is not None
+    assert connector.persist_sync_state_called is False
+
+
 class _FakeDropboxConnector:
     instance = None