NixOS

I personally symlink/hardlink to my dotfiles repo. You can see an example of it here.

NixOS does that well. I never quite managed to figure out a solution to this on other distros (which is actually what led me into making the jump in the end).

Maybe etckeeper fits your use case? It’s specifically built for managing /etc files with version control systems. I can’t say much about it since I’ve never used it, though.

but maybe somebody knows a clever way to handle this?

backups

There should be no dotfiles outside of home directories so I assume you mean a config file. In those cases, git and symlinks are a great option. Make a config directory in your home dir and organize it however you want. Include config files for the tools you’re interested in, commit them to git for backups and then symlink/hardlink the file to the expected path for the application.

@gkpy I assume by “dotfiles” you simply mean “config files” as there should be nothing in your /etc/portage directory that’s hidden. For all configs I want to backup, I just keep a copy of them elsewhere. As for portage stuff, I just copy my make.conf, and everything in each repos.conf and package.* directories.

If you want to simplify a complex solution to an already simple thing, take a look at bare git worktrees.

Not a great solution, but my custom set of functions that synchronize the (dot)files just copy them over into a directory preserving their paths within it e.g. cp /etc/hosts ~/.sysbackups/$(hostname)/etc/hosts