This is still an issue. I don't have a way to work around it, short of approving everything in Jenkinsfiles, which isn't a solution.
In addition, I have more use cases... I need to be able to specify I need submodules for a project.
In case it wasn't clear originally, I'm using the Github Org Folder Plugin, which means I don't have a web-ui where I can add these GitSCM.extenions.
I don't know what the GitSCMSource object is or how to get it. I only have the scm object, which is a GitSCM object.
It seems like there should be a way to modify (some) of the GitSCM object from the Jenkinsfile (not the ref or branch or url).
I would expect to be able to do something like this:
scm.add_extension([$class: 'CloneOption', noTags: false, reference: '', shallow: true]);
Though even that is painful. :-/ I'm not even sure how that would appear (or if it would appear) in the pipeline snippet generator.