That overwrites the remote dotfiles. Any workarounds?

:h netrw

You can also just place config files anywhere if you know what you then load. That's what I do in my dotfiles, but not exactly like the parent. I also purposefully keep the repo size tiny so it's also just easy to clone. I'd recommend setting a env var so you can always just set that

Also don't forget you can have local vim files. I have a function at the end of my vimrc that looks for '.exrc', '.vim.local', '.nvim.local' in the current directory. Helpful for setting project settings.

I've found lnk [0] to be a nice tool for this. Similar to GNU Stow as another comment mentioned, but plays a bit nicer with git (and, in my opinion, is nicer to use).

Edit: just remembered there was a good comparison of lnk and stow on the HN discussion of lnk from a few months back [1].

[0] https://github.com/yarlson/lnk

[1] https://news.ycombinator.com/item?id=44080514

GNU Stow? https://systemcrafters.net/managing-your-dotfiles/using-gnu-...

Keep the alternate sets in different subdirectories.