Abandon hope.

I just treat ~ as a system-owned configuration area, and put my actual files (documents, photos, etc.) in a completely different hierarchy under /.

"/home/${USER}" for whatever junk programs are going to stick there, "/home/${USER}/home" for my "real" home directory.

I have been doing this for decades. My files are in a sub-directory of $HOME. It also makes it very obvious when a piece of software does not treat your $HOME with respect.

You could write a kernel module, then, that just hides certain symlinks from you (which is effectively what this module is).

On Windows this was always easier because, for some reason, most everyone respected %appdata% compared to XDG_CONFIG_HOME, but also because hidden files wasn’t just a naming convention but an actual separate metadata flag.

Always... Except for the decades before this became common. Never a bloated C: root directory. Microsoft even had games store stuff in My Documents\Games at one point. My Documents was a user dir that saw a lot of abuse over the years.

They still have that, it's just `My Documents\My Games` now. And Visual Studio makes a folder in My Documents for every annual release. And…

Yes, as in there’s no reason Linux can’t clean up its game the same way.

That ship has sailed 30 years ago.