Just a quick comment.
Did you edited the configurations and their dependencies by hand? Since some time I never update them by hand, only use versioner to generate a new version for ConfigurationOfGToolkitCore and automatically also update all dependencies to all other configurations that I need. Then I make just one issue to integrate ConfigurationOfGToolkitCore that also loads/updates all other configurations. I know this is still not ideal but it's significant less work than what you described.