For what it's worth, I think the new agent doesn't setup WebSphere correctly. Using the 4.1.2-1053 agent, I could not get the WebSphere Admin server properly detected by the agent until I modified the wrapper.conf file bundles/agent-4.1.2-1053/conf/wrapper.conf:
wrapper.java.classpath.4=/lawapp/WebSphere/AppServer/plugins/*.jar^M
wrapper.java.classpath.5=/lawapp/WebSphere/AppServer/lib/*.jar^M
In other words, it didn't work until I included jar's from both "plugins" and "lib" from the WebSphere Appserver home in the wrapper config manually. I don't see anything in hq-agent.sh that would look at agent.properties and include the right classes, even though I had set websphere.installpath to the correct settings, re-ran setup, deleted the data directory, etc etc.
My test system is down right now for patching, but I'll try to use your notes to cut down on the included jar files. I just didn't feel like working TOO hard to do what the agent was supposed to be doing for me 🙂
With these changes to the agent configuration, I could set up my WebSphere Admin Server in the HQ UI, and it detected my node. It took me a minute to realize I had to go back up to the "platform" level to see the WebSphere node service (it doesn't show up under the Admin Server).
Most of the services underneath "Websphere 6.1 NODENAME server1" are grayed out, but at least I can get JVM memory. (Note, I had to restart the agent to start collecting JVM memory parameters beyond JVM Used Memory.)
I'll start a new thread about how I think the agent doesn't setup the websphere CLASSPATH anymore if nobody responds to this one 😉