I did this for a while. I had to switch to stow when I got a new job that had data security requirements - I had to keep the "work" bits of my dotfiles separate

I did this for a while. I had to switch to stow when I got a new job that had data security requirements - I had to keep the "work" bits of my dotfiles separate from the non-work parts, and so couldn't keep everything in the same git repository. Ended up writing a set of rcs that just imported appropriate .d directories, keeping two git repos, and stowing both of them.