I'm not sure I understand. I use the maven shade plugin, so all there is at runtime is the JVM (system package) and the jar (built from libraries, but all of that's handled nicely with maven and its plugins), which can be fetched by http(s) from the repository and then just run (java -jar xyz.jar). There's no wrapping at the filesystem level but there doesn't need to be, because the classpath lets code load everything it needs from within that one jar file.