Hello,
While you can always manually change any generated files that you like, there are a couple ways to control the behavior before scaffolding:
The first is via the Code Generation section of the Code Generation tab that is shown when the Spring DSL node is double-clicked. Once on the Code Generation tab, you will be able to turn off generation for any artifacts you like.
The second approach is coming very soon in our 8.6.1 release with Customization Projects. This new capability will allow you to customize the templates used in Scaffolding generation. So, for example, you can find all the references to atomikos in the templates and remove/update them with something else. Stayed tuned for this new release coming out very soon.
Kind regards,
Dave