The deployment code is this:

Archive<?> archive = ShrinkWrap.create("test.jar", JavaArchive.class);
archive.as(ExplodedImporter.class).importDirectory("target/classes");
archive.as(ExplodedImporter.class).importDirectory("target/test-classes");

If I pack classes using this technique, then my CDI Extension doesn't fire the ProcessAnnotatedType for classes that are not my test class.
On IRC aslak commented the following:

"it's due to a 'hack' in the WeldEmbedded deployer, it assumes it will get a Archive with ClassAssets.. but when you do import, it wil be FileAssets, so they are ignored"