I use git-annex and Guix (particularly Guix Home in this case) for managing all of my data, including dotfiles. git-annex handles syncing (and backups via delivery to a Borg repo) and version management as git does, while Guix takes care of installing programs and setting up configuration files.

I previously wrote a custom Guix service that utilized Stow as well for managing writable files, but have since replaced it with another custom Guix service that handles some cleanup processes better.

Depending on how much you want simplicity of restoration, this approach might be on the heavier side since it’s concerned with a lot more than just dotfiles. You could replace git-annex with git to simplify the syncing part if you’re only interested in managing configuration files, though. Here’s what my Guix config looks like; the readme file shows how I would set up a system from scratch.