I thought we would be reusing the Jandex index loaded/created by ORM

Sure, that's also a plan, but completely unrelated. The biggest junk of work for getting rid of commons-annotations is to let the programmatic configuration instantiate our meta model classes directly, instead of going via pseudo annotation created by common annotations. In the latter case the pseudo annotation then get processed by the AnnotationMetadataProvider and turned inot meta model classes. Seems natural to go directly to the meta model, especially since the programmatic API is much more regular compared to the annotations.