Hi again,
The JPackage people have the following solution: They include the JBoss patches into their source and produce two independent non-conflicting binary packages from the same source package:- one unpatched for general use (that goes into /usr/share/java) and- one for jbossas (which goes into /usr/share/java/repository.jboss.com/) together with some metadata about the jar that is used by jbossas and the patch applied (for documentation).
I have just discussed this with the JPackage people who answered my question.
JPackage enable different build and runtime setups for the moment being as there are conflicting (gjc-compiled) versions of jars in /usr/share/java in the Fedora 9 base install that cannot be used for jboss build but work in a runtime setup. So the different versions really come from different source packages. It is not at all intended to produce different binaries from one source package.
JPackage is working on merging the conflicting source packages to get one and only one binary.
So this is what I'll work on as well. No need for any "workaround". Florian