[jon@jon-laptop ~]$ xdg-app install --user nightly org.mypaint.MypaintDevel
145 metadata, 1496 content objects fetched; 39082 KiB transferred in 106 seconds
[jon@jon-laptop ~]$ xdg-app run org.mypaint.MypaintDevel
create extra dir home/jon/.var/app/org.mypaint.MypaintDevel/config/user-dirs.dirs: Not a directory
This on Arch Linux, with xdg-app 0.4.12.
org.gimp.GimpDevel on the same system works.
Issue was also present with xdg-app 0.4.11, and earlier version of MyPaint devel.
Hmm, possibly this was a bug in an older version of xdg-app or the bundle. Cause when I do "rm -rf /home/jon/.var/app/org.mypaint.MypaintDevel", then try to run again - it works.
I guess we can close this then...