With the change introduced by SHRINKWRAP-505, it doesn't cover the following situation.

If I have a JarArchive that contains classes at the root, as its a jar, but if it happens to have files places in '/WEB-INF/..' then this change makes the assumption that all classes should be found in '/WEB-INF/classes/'.

Where it scans for packages shouldn't rely on the presence of a file at a particular location, but try each and see which actually succeeds.