I ran into this issue when working with Arquillian and Weld EE 1.1 Embedded container (that uses ShrinkWrapClassLoader under the hood). ShrinkWrap correctly builds web archive with CDI extension (using org.jboss.shrinkwrap.api.container.ManifestContainer.addAsServiceProvider(Class<?>, Class<?>...); this was also discussed in SHRINKWRAP-266).

Output:

test.war
/WEB-INF/
/WEB-INF/classes/
/WEB-INF/classes/META-INF/
/WEB-INF/classes/META-INF/services/
/WEB-INF/classes/META-INF/services/javax.enterprise.inject.spi.Extension

However no extensions are found. org.jboss.shrinkwrap.api.classloader.ShrinkWrapClassLoader probably does not find any resource when looking for "META-INF/services/javax.enterprise.inject.spi.Extension".

Note that I'm not quite sure whether it's ShrinkWrapClassLoader or WeldEEMockContainer issue.