@adamw @b0rk @angermcs to apply the files i do the following

1. git clone --bare <repo url> .dotfiles
2. alias dotfiles='git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME'
3. dotfiles checkout
4. source ~/.zshrc

1. creates a bare clone
2. creates an alias for working with you dot files repository - good idea to also put this same alias in .zshrc
3. actually checkout the files from the repo, if you have issues here you may need to stash before checking out
4. source the shell configuration