Instructions copied from the following article:
The Best Way to Store Your Dotfiles a Bare Git Repository Explained
Which is based on this article:
Dotfiles: Best Way to Store in a Bare Git Repository

Overview of Storing Dotfiles in a Git Repository

• Set a Git repository’s work tree to $HOME
• git add and commit your dotfiles to the Git repository. The dotfiles remain at their original paths.
• Push your Git repository to a remote server such as GitHub. Now your dotfiles are backed up, and can be replicated.

Replicate your dotfiles by cloning down the repo, configuring it, and checking out the files. The files are checked out at their original paths relative to $HOME.

Creating local repo:

1. git init --bare $HOME/.cfg
2. alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'
3. echo "alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'" >> $HOME/.bash_aliases
4. config config --local status.showUntrackedFiles no
5. config add <files> + config commit -m "add things"

Getting existing repo:

1. echo ".cfg" >> .gitignore
2. git clone --bare <remote-git-repo-url> $HOME/.cfg
3. alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'
4. config config --local status.showUntrackedFiles no
5. config checkout

Line by line breakdown

Creating Local Repo

1. git init --bare $HOME/.cfg
   Create the folder .cfg, a bare Git repository which will be used to track our dotfiles.

2. alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'
   Create an alias named config which allows you to send Git commands to the .cfg repository from any location, even outside of the repository. It also configures the initially bare .cfg repository to set $HOME as the work tree, and store the Git state at .cfg.

3. echo "alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'" >> $HOME/.bash_aliases
   Make the config alias permanently available.

4. config config --local status.showUntrackedFiles no
   Only show config files manually added, not every file under $HOME.

5. add, commit and push to the remote
   Use the config alias to add and commit files from any directory.
   config remote add origin <remote-url>
config push -u origin master

Install Your Dotfiles on a New System

1. echo ".cfg" >> .gitignore
   There could be weird behaviour if .cfg tries to track itself. Avoid recursive issues by adding .cfg to your global Git ignore.

2. git clone --bare <remote-git-repo-url> $HOME/.cfg
   Clone the dotfile repo to your .cfg directory.

3. alias config='/usr/bin/git --git-dir=$HOME/.cfg --work-tree=$HOME'
   Set up an alias to send Git commands to .cfg, and also set $HOME as the work tree, while storing the Git state at .cfg

4. config config --local status.showUntrackedFiles no
   Set a local configuration in .cfg to ignore untracked files.

5. config checkout
   Checkout the actual content from your dotfile repository to $HOME.
   config checkout might fail with a message like:

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

   Git doesn’t want to overwrite your local files. Back up the files if they’re useful, delete them if they aren’t.

Programs used

In no particular order:

• alacritty
• i3
• i3status
• nvim
• picom
• feh