~/.config/user-dirs.dirs you can change the user folders. But do they actually do anything except for changing the links in Nautilus? I can see that changing
XDG_DESKTOP_DIR does something – namely it changes the contents of which folder are displayed on the desktop, as expected – but does anything else do something?
These are special locations as defined by freedesktop.org, and so is used by many programs, not only nautilus. They will be used by any file manager (dolphin, Thunar) and by apps - the Music directory by music players, Downloads by browsers, Documents by text editors, etc.
xdg-user-dirs is a tool to help manage "well known" user directories like the desktop folder and the music folder. It also handles localization (i.e. translation) of the filenames.
The way it works is that xdg-user-dirs-update is run very early in the login phase. This program reads a configuration file, and a set of default directories. It then creates localized versions of these directories in the users home directory and sets up a config file in $(XDG_CONFIG_HOME)/user-dirs.dirs (XDG_CONFIG_HOME defaults to ~/.config) that applications can read to find these directories.
There is a nice discussion on the Arch wiki , see https://wiki.archlinux.org/index.php/Xdg_user_directories