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In JBoss AS 6, one can change which JSF implementation JBoss AS uses by editing /deployers/jsf.deployer/META-INF/jsf-integration-deployer-jboss-beans.xml. JBoss bundles Mojarra 1.2, 2.0 and MyFaces 2.0 by default.
However, if one changes this, JBoss tools keeps putting the two hardcoded libs in /deployers/jsf.deployer/Mojarra-2.0/jsf-libs on the IDE's lookup path. This means that stepping through JSF source code is totally broken then.
A workaround is to copy the libs from the other configuration to /deployers/jsf.deployer/Mojarra-2.0/jsf-libs and rename them to jsf-api-2.0.3-b05.jar and jsf-impl-2.0.3-b05.jar. This works, but there is something unsettling of having e.g. the 2.1.2 libs called 2.0.3 just for the sake of the ability to debug.