とりあえず特にこちらで何も出力しないで実行してみました。

Whoops, looks like something went wrong.
1/1 ORMException in ORMException.php line 259: The identifier id is missing for a query of Eccube\Entity\Order

in ORMException.php line 259
at ORMException::missingIdentifierField('Eccube\Entity\Order', 'id') in EntityManager.php line 378
at EntityManager->find('Eccube\Entity\Order', array('id' => null), '0', null) in EntityRepository.php line 154
at EntityRepository->find(null) in ShoppingController.php line 336

at ShoppingController->complete(object(Application), object(Request))
at call_user_func_array(array(object(ShoppingController), 'complete'), array(object(Application), object(Request))) in HttpKernel.php line 144
at HttpKernel->handleRaw(object(Request), '1') in HttpKernel.php line 64
at HttpKernel->handle(object(Request), '1', true) in Application.php line 586
at Application->handle(object(Request)) in Application.php line 563
at Application->run() in index_dev.php line 117

何がなにやら・・です。
ShoppingController.phpのfunction completeでセッション削除前にIDとってますが、その前に消えちゃってるということでしょうか。