As with JBoss EAP5.x, I have the habit of working in a copy of a 'profile' directory. With JBoss AS7/EAP6 I therefore work in copies of 'standalone' and 'domain' (depending on the operational mode). When I start AS/EAP, I reference the correct server directory with the 'jboss.server.base.dir' or 'jboss.domain.base.dir' system property. This allows me, among other things, to run multiple AS/EAP instances from a single JBoss AS/EAP installation.
It seems that the JBDS AS7 plugin only allows me to reference the default 'standalone' directory. I'm not able to select a different directory in the 'JBoss Runtime' configuration screen. I would propose to add the possibility to start a JBoss AS7/EAP6 instance from a different directory than 'standalone'.