This issue is a regression of
SHRINKWRAP-186. The location of the ManifestContainer for a WebArchive should be /WEB-INF/classes/META-INF, not /META-INF. This location is backed up by our target locations per archive type page.
A sample use case is bundling a persistence.xml in a web archive:
This also breaks the ServiceLoader registrations, as they appear in /META-INF/services/ rather than in /WEB-INF/classes/META-INF/services/