File structure of directory follows location of where the files should be in relation to $HOME.
GNU Stow can be used to auto-link files to where they belong. Simply run stow .. If there are existing files causing conflicts, stow --adopt . and pull from the repository to ensure any overwrites don't stick.
This video provides a great simple explanation on stow.
Note: stow will directly link directories if those don't exist, which may
cause files to then be added to .dotfiles if a program creates them in the
directory (e.g.: any other configuration files are created under .config/xxx).
To avoid this, create any directories needed first, then run stow . to just
link the files