Initial setup

For a system previously using a plain git repo:

rm -rf $HOME/.git
git clone --separate-git-dir=$HOME/dotfiles.git git@github.com:bwalex/dotfiles.git $HOME/dotfiles-tmp
git --git-dir=$HOME/dotfiles.git --work-tree=$HOME status

# Restore/etc files as per status

After initial setup & reloading shell config:

dotfiles config --local status.showUntrackedFiles no
dotfiles submodule update --init --recursive
rm -rf $HOME/dotfiles-tmp

Generally, use dotfiles as if it was git.