my application needs multiple jars to work. Since it is a desktop application i can not hold the user responsible of installing. So in my build script i unzip the jars conte
Well you're throwing away the MANIFEST of your third party jars, so that could cause you problems. For example you could be causing security issues by throwing away the "Sealed" attribute.
Why not just create a simple installer and a script to launch your application which sets the CLASSPATH correctly?