~$ cat .config/user-dirs.dirs
XDG_DESKTOP_DIR="$HOME/"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_DOCUMENTS_DIR="$HOME/doc"
XDG_MUSIC_DIR="$HOME/media/music"
XDG_PICTURES_DIR="$HOME/media/pictures"
XDG_VIDEOS_DIR="$HOME/media/videos"
XDG_TEMPLATES_DIR="$HOME/.templates"
XDG_PUBLICSHARE_DIR="$HOME/.public"

~$ xdg-user-dirs-update
/home/josh/.templates was removed, reassigning TEMPLATES to homedir
/home/josh/.public was removed, reassigning PUBLICSHARE to homedir

~$ cat .config/user-dirs.dirs
# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="$HOME/"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_DOCUMENTS_DIR="$HOME/doc"
XDG_MUSIC_DIR="$HOME/media/music"
XDG_PICTURES_DIR="$HOME/media/pictures"
XDG_VIDEOS_DIR="$HOME/media/videos"
XDG_TEMPLATES_DIR="$HOME/"
XDG_PUBLICSHARE_DIR="$HOME/"


Please don't overwrite my configuration.

- Josh Triplett

Dear Maintainer,

I have the same problem. Why was this never fixed?

What makes it worse is that a comment is added 'All local changes will be retained on the next run.' but this is not true. The changes are not retained.

Maybe you want to create the missing directories but do not change the
configuration when you have promissed not to do so.

Cheers,

Ronny