using the same repo with different OS

I have my repos on a USB key (fat32 fs) and I work with git under
linux and windows (maybe also Solaris in the future).

Considering also the new MinGW port, should I use a different repo for
every OS I work with???

Are planned/expected OS-specific files in the repo preventing me to
use the same whenever I'm working???

thanks in advance

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Stefano Spinucci