vim with Windows developments under linux and git

I have the usual problems with ^M and some other ones in these cases.

I vant to use vim to develop Windows apps under linux (building in
some Windows VM), with vim under linux.
I do not want to get rid of ^M, I want to keep all my files in some
specialized directory in Windows format managed by git and vim.

Is there somewhere an howto for "good practices", particularly to set
vimrc ?

And, cerise sur le gateau, vim should remain correct for normal linux
files...

Thanks
PC

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