Some time ago, I did some research on a tool called Java2Exe which converts jar files to an executable and obfuscates or encrypts the file names to deter reverse engineering. In this blog post, I show how to recover the jar archive at all 3 protection levels. I hope you enjoy.
http://reverseengineeringtips.blogspot.com/2014/12/unpacking-jar2exe-21-extracting-jar.html