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For servers that have >1 target per instance it is not enough to identify the server instance (note the call in DeploymentManager takes a list of targets as a parameter). Not a problem for tomcat or PE but potential problem for app server. This will also require change in j2eeserver (Deployment.java).
Actually maybe it makes sense even for tomcat to represent multiple hosts. Supporting this for tomcat can be done separately but it would take advantage of this being solved.
Too big change for 4.0 (requires API change).