I keep a .dotfiles git-repo similarly. The configs/custom scripts/etc are organized into separate folders by what they do (shell config/work tools/...) and I use GNU Stow to symlink them into my home directory. Makes setting up super easy:

    git clone <repo> .dotfiles && cd .dotfiles
    stow --target=$HOME --dir=packages shell-config
    stow --target=$HOME --dir=packages work-stuff

I've found this to be much more manageable than tools like yadm since I can pick-and-choose sets of configs/scripts based on the machine I'm using them on.