Stolen from https://developer.atlassian.com/blog/2016/02/best-way-to-store-dotfiles-git-bare-repo/

Setup

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

Example usage

config status
config add .vimrc
config commit -m "Add vimrc"
config add .bashrc
config commit -m "Add bashrc"
config push

Installation on new machine

Prior to the installation make sure you have committed the alias to your .bashrc or .zsh:

alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'

And that your source repository ignores the folder where you'll clone it, so that you don't create weird recursion problems:

echo ".cfg" >> .gitignore

Now clone your dotfiles into a bare repository in a "dot" folder of your $HOME:

git clone --bare <git-repo-url> $HOME/.cfg

Define the alias in the current shell scope:

alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'

Checkout the actual content from the bare repository to your $HOME:

config checkout

The step above might fail with a message like:

error: The following untracked working tree files would be overwritten by checkout:
    .bashrc
    .gitignore
Please move or remove them before you can switch branches.
Aborting

This is because your $HOME folder might already have some stock configuration files which would be overwritten by Git. The solution is simple: back up the files if you care about them, remove them if you don't care. I provide you with a possible rough shortcut to move all the offending files automatically to a backup folder:

mkdir -p .config-backup && \
config checkout 2>&1 | egrep "\s+\." | awk {'print $1'} | \
xargs -I{} mv {} .config-backup/{}

Re-run the check out if you had problems:

config checkout

Set the flag showUntrackedFiles to no on this specific (local) repository:

config config --local status.showUntrackedFiles no

You're done, from now on you can now type config commands to add and update your dotfiles:

config status
config add .vimrc
config commit -m "Add vimrc"
config add .bashrc
config commit -m "Add bashrc"
config push