The double prefix comes from the fact that we specify the prefix in the configure and the DESTDIR in the install. Some, but not all, of the files are, effectively, installed into $DESTDIR/$prefix/<…>. Unfortunately some of the files are only installed into $DESTDIR/<…>. I had a look at trying to fix that, unfortunately, this is a result of a maze of twisty little passages, all alike. I was afraid of being eaten by a grue, and so decided to just move the swig lib files that ended up in the wrong place after the install.