git multisite setup

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Hi,
In my sites folder i have folders for different sites of mine:
example.com example2.com, and i also have generic files like an
includes dir and a .htaccess file that all sites use. what is the best
way to track the generic files and the different sites?

i was thinking each site has its own .git repo. and then make a .git
repo for my sites folder but ignore the individual sites dirs.
actually that's what i'm doing now.

should i use submodules? i don't really understand submodules and the
examples i saw did not cover nested folders

Thanks!

matt
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