New applications should be created with json serializer

The fix introduced at 75ba7425f6d235f254c00a45a58f42e88f80301a were
missing this case.

To fix the original issue mentioned at that commit the correct is to
remove update_config_files from the command list since we should not run
both config_files command when creating a new application.

Tests were added to make sure everything is working fine.