Set things up with a bare git repository. This technique has been described in many different ways.
git clone --bare git@github.com:mtcrutch/dotfiles.git ~/.dotfiles.git
alias dotfiles='git --git-dir=$HOME/.dotfiles.git/ --work-tree=$HOME'
dotfiles config --local status.showUntrackedFiles no
dotfiles checkout
dotfiles submodule update --init --recursive