My dotfiles, organized by machine. Each top-level folder mirrors $HOME for that computer.
Each folder's contents are meant to be symlinked into $HOME on that machine. The simplest way is with GNU Stow:
stow -t "$HOME" -d . fragata # on the laptop
stow -t "$HOME" -d . isidorus # on the desktop
If the files already exist in $HOME, add --adopt to move them into the repo and replace them with symlinks (then check git diff).
Or, if you prefer the bare-repo approach, see fragata/README.md for the original setup instructions (point --work-tree at the machine's folder instead of $HOME directly).