One of my favorite #nextcloud apps is called "Keep or Sweep". All it does it show me a random file (maybe one I haven't opened in a while) and ask me if I want to keep it or not.
I love it! I wish there was something similar for the desktop that would go through my old files and that it would ask me if I wanted to move the file to somewhere else, to help me keep my files organized.
Really the core issue is also that the home directory filesystem idea is a bit silly by design.
Per application files (think executables and dotfiles) don't need to really be managed by external applications- they take care of themselves.
Files we do use between applications (documents, photos, etc.) aren't well organized in a simple hierarchy. Good indexing systems (tagging, full text search, etc.) is much better for such files.
Emacsen