The 'naked linux program' is just a gzipped tar file. It comes with the .jar files and a runlime.sh shell script. You have to run this script in the same directory as the jar files hence the replacement runlime.sh script business. I installed LimeWire this way too and wrote an alternative script for my own use. You can see it at:

http://www.cyberspace.org/~kohl/limewirelinuxhowto.html

The howto was written for 1.7 and probably could use updating now (re where to download). I'll get around to that in the next couple of weeks.