Edit: Damn, just noticed the full path in your post which makes most of the below irrelevant but I've decided to leave it in case some noob follows your footsteps.

~ stands for home directory and is different if you are user or root.
For user, ~ is /home/user. To avoid confusion, try
The easiest way to get there is by using automatic expansion. Type cat, space, slash, h, then click Tab in the X Terminal tool bar (to expand h to home/), u, Tab again, dot, co, Tab, u, Tab. If that does not expand to /home/user/.config/user-dirs.dirs then you are in trouble. You can copy the text in the code block in peterleinchen's post to a file, name the file user-dirs.dirs and copy it to /home/user/.config, but I wonder if that file is missing what else is.