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.

http://community.jboss.org/wiki/Containerrootsperspecarchive

A sample use case is bundling a persistence.xml in a web archive:

WebArchive war = ShrinkWrap.create(WebArchive.class, "test.war")
   .addAsManifestResource("test-persistence.xml", "persistence.xml");
System.out.println(war.toString(true));

Current output:

test.war
/META-INF/
/META-INF/persistence.xml

Expected output:

test.war
/WEB-INF/
/WEB-INF/classes/
/WEB-INF/classes/persistence.xml

This also breaks the ServiceLoader registrations, as they appear in /META-INF/services/ rather than in /WEB-INF/classes/META-INF/services/