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Where exactly is the lucence-core 2.2.0? It's not being shipped in JBoss AS. So ideally, each app should package that within the application.
That is likely to be the problem - I am using a modified JBoss installation that has been split into two to keep jboss code separate from our code and then classpath entries added to the \server\reims\conf\jboss-service.xml so that addition classpath directories are included.
I have taken a different approach - it seems pebble ships with it own versions of org.w3c.dom and org.xml.sax code which also comes with the JDK in endorsed folder. This is the conflict that I was trying to avoid by isolating the classloading. By removing this code and using the endorsed code I no longer need to isolate as the standard war classloading policy works and my problems go away.