~/Other People # containing one directory for every person; synced to Nextcloud
  ~/Documents    # most of my personal stuff; synced to Nextcloud
  ~/Downloads    # symlink to ~/Local/Downloads
  ~/Local        # Everything that is unimportant
  ~/Projects     # containing one git repository per project
  ~/Skripts      # various scripts I use; synced to Nextcloud

Photos are on a separate NFS device. In addition, there are various .* directories, like .vim, .R, .golang, etc. and some of them are being synced to the Nextcloud too. I don't sort by filetype anymore. So I don't care if it is a PDF or something else, but instead, I care about the context: Is it an ebook, a scan, or does it belong to some project?