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When starting JBoss 4.0.3sp1 in the all mode which enables clustering a parameter needs to be passed to bind jboss to the right ip address. When starting JBoss adding a server parameter -b <ip address to bind to> would work for this. I am not sure for stopping JBoss through netbeans, in the JBoss start/stop bash scripts I know you can add a -s <ip address bound to> to the shutdown line. In netbeans 5.0 beta-2 there is a field for host and port but they are read-only and there is no field to add server parameters. JBoss will not start correctly (clustering will fail) in the all configuration if the address is not bound. Also there seems to be no way of telling where you want to deploy your application to. For example with the all configuration you should be able to deploy to the farm directory or to the deploy directory.
-> jboss
I filed and fixed the issue 70135 which avoids the mentioned exception. However, it does not provide any new configuration possibilities in the IDE. It's a matter of the future release(s) planning.