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I've had a look at this. Here is my interpretation, which, as a total newbie to weld may be totally misconceived!
The only use of AnnotationDiscovery that i can find is for resolving observer methods that use @WithAnnotations when firing ProcessAnnotatedType events. These observers can mark a PAT as vetoed but the class will have already been loaded.
Are you proposing adding a new method to AnnotationDiscovery? Say Set<String> getVetoedClasses(), call it before BeanDeployer.addClasses and use the resulting set to filter the classes added by BeanDeployer.addClasses?
If this is the case i suppose that SimpleAnnotationDiscovery should just return an empty list and an extensions using annotation indexes would implement it to return a meaningful result?