I recently had a problem which may cause some real issues with user. Please allow me to explain the background:
I installed a new computer a couple of days ago (Fedora 31). I started out with an empty home directory and I did not install Emacs from the repositories. Instead, I installed all the build dependencies and built Emacs master from Git.
After installing Emacs, and starting it once to check that it worked, I checked out my $HOME/.emacs.d directory from source control and started Emacs. At this point, I noted that my init file was not being loaded.
After checking all the obvious things, I remembered seeing something about supporting the XDG standards, and because of this I found a directory $HOME/.config/emacs. This directoriy contained a single file whose name I cannot remember. As far as I can rceall, this file was empty. I deleted this directory and restarted Emacs. At this point my init file was loaded correctly.
If I had not known about the XDS stuff, I would have been extremely confused about this behaviour. I don't think it can be expected that users know about this, do this could cause a lot of confusion among people following tutorials for example.
I'm guessing that the $HOME/.config/emacs directory was created when I started Emacs before checking out my .emacs.d from source control.
Would it make sense to display a warning before creating this directory in the first place, explaining that doing so will prevent $HOME/.emacs.d/init.el from being loaded?