Just to clarify something. You don't *have* to be in the LimeWire directory for LimeWire to work. The only reason you start LimeWire from the LimeWire directory when you use the provided runlime.sh is because it only uses the current directory as the class path:

java -classpath . RunLime

If you add the correct classpaths when you're starting up limewire, you can start it from anywhere.