Strange.
/usr/lib/cider/Cider is from their build and its upper case in any OS they support. Which is fine.
The /usr/bin/cider symlink is lower case (everything in /usr/bin/ is lowercase)
So for my I just changed the desktop file as described in github issue. Nothing more to do.
The only reason you need absolute path in desktop file is that the location of the executable is not in the path.
This is the case here but /usr/bin/cider symlink should solve this. Its not wrong to put /usr/bin/cider in exec but should not be needed.
/usr/bin is in the path of every linux distro.