Always write out new ref if different from old

Previously a new ref was only written if the validation failed. Now it is always written if different. In addition, add a check whether the preprocessor is idempotent (might lead to failures in downstream projects if dedicated problematic preprocessors are used).

Also, add workaround for gaudi/Gaudi#108 which is a follow up from !2260 (merged) (the bug got manifested in the brunel-upgrade-paramKalman-auxiliaries test)