It's worth noting that before he worked on Loom, Ron Pressler wrote Capsule, which is a kind of uber-fat-jar system that embeds JARs within JARs:
https://github.com/puniverse/capsule The website is offline now but it had a lot of features, including the ability to extract shared libraries from the 'capsule'. It worked by extracting files to a cache directory and running them from there. So, Ron might have some insight to offer here, if asked.
