This is exactly what I do and I think it works fantastically. I also have the same problem with initial clone and I keep meaning to write a script to automate i

This is exactly what I do and I think it works fantastically. I also have the same problem with initial clone and I keep meaning to write a script to automate it (especially in a push sort of way where I just specify the host that I want to convert and it does it over ssh with git push). I also make an effort to push my config files into .config wherever possible. I really hate the ~ dotfile clutter.