My Nautilus is showing the "Desktop" entry twice. I assume that it is using some kind of configuration mechanism, maybe there is a .desktop file sitting somewhere in my home folder that is creating this but I am not sure where to look.
So which file locations or dconf keys is nautilus using to populate this list?
You can edit them by modifying ~/.config/user-dirs.dirs.
Moreover, you can also check if the second Desktop link is a bookmark by opening the bookmarks file in ~/.config/gtk-3.0/bookmarks.
According to How do I remove 'Places' entries from the Nautilus sidebar? user-dirs.dirs file is generated from the user-dirs* files in /etc/xdg.
The following screenshot shows one of the "Desktop" entries to be renamed to "Download" after I changed the entry XDG_DOWNLOAD_DIR to something different than $HOME/Desktop. As can be seen, the Desktop entry with the downward arrow changed its label back to Downloads.
