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I have similarly large builds, and don't have a problem with our clean scripts leaving files behind, so it's certainly not 'impossible'.
In any event, if you really want a workspace for each branch, and don't want to use branch switching as I suggested earlier, then why not have one job per branch? That'll let you run builds in parallel as well, and more easily identify what code is actually being built. The way you are trying to do it seems like it would only confuse you and your users.