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The .class files created after the interweaving are not marked as derived. So, when you call IResource.isDerived(), it returns false. These should be marked as derived like the .class files generated by the javac build ... then the behavior will be consistent. This causes problems for other plug-ins which use isDerived() to determine what to do with the resource. My understanding is that all that needs to happen is to call IResource.setDerived(true) on the generated .class files. Thanks.
something AJDT should be doing post build.
fixed - with 101489 being addressed.