Right now the only breaking api change seems to be around ChannelManager going to RepoManager, and presumably associated domain objects were also changed. More details are: http://rhq-project.org/display/RHQ/API+Changes+Between+JOPR+2.3.1+And+RHQ+3.0.0
This will need updating too... http://www.redhat.com/docs//en-US/JBoss_ON/2.3/html/Installation_Guide/Installation_Guide-Working_with_the_CLI-Implicit_Variables.html
I made a section in the release notes for "structural changes" here: http://elladeon.fedorapeople.org/jon-drafts/3.0/rel-notes/changes-in-behavior.html I also updated the names of a couple of the variables in http://elladeon.fedorapeople.org/jon-drafts/3.0/cli/Working_with_the_CLI-Implicit_Variables.html.
Verified.