I use GNU Stow, and so the directories are set up for that, however, you can manually move them to where the respective files need to be
To use Stow use
git clone https://github.com/nectariner/dotfiles.git ~/
cd dotfiles
stow nvim #or whatever configuration files you want to use
NOTE: this may give some errors if you already have configuration files for a given application, to fix you can just delete the configuration files you already have and just use stow again