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I'm sure how you go about doing this would differ depending on what program you're using, but I would imagine there is some way to "ignore" certain files/folders and then you should set the build directories and bin directories to be ignored, that way you can build it on each machine and it won't propigate to the other machines.

That said, I use Mac's solution myself, but if you want to continue using what you're using I think my answer is the way to go, assuming it is supported by whatever software you are using.