My dotfiles git repo is meant to be cloned in my home directory. It comes with this .gitignore committed in the repo:
/*
!/.vim/
/.vim/.netrwhist
Basically it ignores everything in my home directory, unless I explicitly `git add` it, which matches my workflow. For the few cases where I want to notice changes (like the entire ~/.vim/ subdirectory), I explicitly un-ignore it as you can see above.The only downside I've experienced is my bash PS1 prompt shows the status of the dotfiles repo (branch/dirty/etc) in any directory I'm in that's inside my home dir - I've learnt to ignore it, and it doesn't interfere with CDing into an actual directory that's its own git repo.