I use these exclusively on the latest version of macOS and don't pull them down enough to verify that they can be cloned without issues arising.

git init --bare $HOME/.dotfiles
alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME'
dotfiles config --local status.showUntrackedFiles no
echo "alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME'" >> $HOME/.bashrc

1. alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME
2. echo ".dotfiles" >> .gitignore
3. git clone --bare --recursive https://github.com/michaeljdeeb/dotfiles.git $HOME/.dotfiles
4. alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME
5. dotfiles checkout

Source: The best way to store your dotfiles: A bare Git repository

To safely delete ~/README.md locally, run dotfiles update-index --assume-unchanged README.md If you need to update README.md, run dotfiles update-index --no-assume-unchanged README.md

For example, installing vim-airline:

cd ~/.vim/bundle
dotfiles submodule add https://github.com/vim-airline/vim-airline

For example, upating vim-airline:

cd ~/.vim/bundle/vim-airline
dotfiles pull

dotfiles submodule update --recursive --remote

For some reason, the above command does not properly update YouCompleteMe and the following additional steps must be done.

cd ~/.vim/bundle/YouCompleteMe/
git submodule update --init --recursive
./install.py --tern-completer

For example, removing vim-airline:

cd ~/.vim/bundle
dotfiles submodule deinit -f vim-airline
dotfiles rm -rf vim-airline