Allow for stages to be removed but jobs to still exist for missing stages

Currently right now if you have any jobs for stages that aren't listed under staging gitlab-ci throws an invalid YAML error and fails immediately. Because I'm trying to template a lot of my gitlab-ci.yml we try to keep all our jobs configured and then update the stages as necessary to call whichever jobs we need. In doing so if you have stages for say lint, validate, test but jobs for lint, validate, test, acceptance it fails because acceptance is missing from the stages array. I think it's useful to throw warning "possibly" that you have jobs configured for stages not called but to throw a invalid YAML error and fail seems too restrictive. Is there anyway around this?