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So, I'm a developer with brew installed along with several other programs installed from source(openCV, boost etc.). I want to do a clean install of OSX(to get rid of some other issues as well), then restore from a time machine backup(I have important apps and files I need to restore). Is there any way I can exclude my user installed command line tools from the restore? (effectively, starting afresh there?)

EDIT: I've just discovered you can exclude the system folder. This should do the trick, right?

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So, in totality, deselecting "System" worked. I now have a clean slate, while the rest of my apps still work.

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