IMHO part of the issue seems to be the question without any context. I believe people would be more helpful if they had explained what they wanted to do and how GIMP wasn’t the right tool for that specific task. It’s what would make me ignore the question (not scold people, no need).
I very much understand how one can think this would revert any changes done to files under version control but not delete the ones that are not. I believe this dialog has since been updated to explicitly state that fact.