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I think git.clean() can't be switched method to always use "clean -xffd" instead of "clean -xfd" because that may damage existing use cases which depend on the current behavior.
I haven't been able to find any better solution than the solution you've proposed. I agree with your recommendation that we should add "Clean before checkout" as an additional behavior. We'll rely on users to choose which ever of the two best meets the need of their use case.
I think we'll still need the switch branch of submodule before checkout pull request as well, but I think that "Clean before checkout" is also a needed addition to the git plugin.
Over the course of the next week, I'll perform some additional tests to better understand the impact of the change.