Description of problem: It is difficult to upgrade artifacts with external jandex files, in the case of RPMs we could not find a proper way of doing it. Following Jason Greene suggestion we moved the creation of the jandex indexes to inside the JAR files META-INF in the build of the components themselves. John Casey worked with Jason Greene to create a maven plugin for jandex (now in upstream jandex AFAIK). As a consequence, the product build should no longer produce external jandex indexes as the components will have their indexes already in META-INF.
PR against the 6.x branch: https://github.com/jbossas/jboss-eap/pull/32
Verified during EAP-6.1.0-ER4 test cycle, none of jandex found as external FS entities.