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 --dotfiles --no-folding .. If there are existing files causing conflicts, stow --adopt . and pull from the repository to ensure any overwrites don't stick. The --dotfiles flag allows for .<something> files to be named dot-<something> within the repository, thus avoiding hidden files, and the --no-folding flag makes it so only directory contents are symlinked, and not directories themselves.
This video provides a great simple explanation on stow.