Storing and linking of dotfiles using GNU Stow.
Create a directory, inside the repo, with the name/configuration to be stored. Create the remaining directories of the chain where you configuration should be linked. For example (from inside the dotfiles directory):
i3's configuration is at ~/.config/i3/config, so create a new directory path inside dotfiles replicating this structure:
mkdir -p i3/.config/i3
Move the configuration file to the new location:
mv ~/.config/i3/config dotfiles/i3/.config/i3
Have GNU Stow create the symlink in the appropriate directory:
stow i3
This is based on the following guide: http://brandon.invergo.net/news/2012-05-26-using-gnu-stow-to-manage-your-dotfiles.html