on gentoo for example I have accrued a few files under /etc/portage
that to my knowledge just have to live there…
right now I basically rely on my backups for this. but maybe somebody knows a clever way to handle this?
NixOS
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.
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).