In installed JON Beta 1 on a RHEL box where Beta0 was running successful for some time. I did not stop the agent for the install.
After the B1 server was up and running, the agent connected and the server told it that it is too old. Agent then tried to self update, which failed and I ended up with no agent running.

RHEL 5.5, sun jdk1.6, pg8.4

> This version of the agent is not supported by the server - an agent update must be applied
The agent update thread has started - will begin the agent auto-update now!
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
This version of the agent is not supported by the server - an agent update must be applied
The agent will wait for [0] threads to die
Downloaded the agent update binary to [/home/hrupp/rhq-enterprise-agent-3.0.0.Beta1.jar]
Missing the envvar [RHQ_AGENT_JAVA_EXE_FILE_PATH] - will try to find a Java executable to use.
Will use the Java executable [/usr/lib/jvm/java-1.6.0-sun-1.6.0.20/jre/bin/java]
Now executing agent update - if all goes well, this is the last you will hear of this agent: [ProcessExecution: executable=[/usr/lib/jvm/java-1.6.0-sun-1.6.0.20/jre/bin/java], args=[[-jar, /home/hrupp/rhq-enterprise-agent-3.0.0.Beta1.jar, --pause=20000, --update=/home/hrupp/rhq-agent]], env-vars=[null], working-dir=[/home/hrupp], wait=[0], capture-output=[false], kill-on-timeout=[false], executable-is-command=[true]]
[hrupp@pickeldi rhq-agent]$ jps
24376 Jps
26723 Main
9353 Main
23340 Main


server console:

10:28:35,362 INFO  [CoreServerServiceImpl] Agent [pickeldi][3.0.0.Beta0(a2b6884)] would like to connect to this server
10:28:35,365 WARN  [CoreServerServiceImpl] Agent [pickeldi][3.0.0.Beta0(a2b6884)] would like to connect to this server but it is not supported
10:28:35,769 INFO  [CoreServerServiceImpl] Agent [pickeldi][3.0.0.Beta0(a2b6884)] would like to connect to this server
10:28:35,772 WARN  [CoreServerServiceImpl] Agent [pickeldi][3.0.0.Beta0(a2b6884)] would like to connect to this server but it is not supported


I was also having agent upgrade issues with agent upgrades on OS X, but attributed it to OS X


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As the above was with an agent that was not started with the wrapper, I thought this may be the case, so I started it with the wrapper script and it started to try to upgrade, but it is now caught in a loop 

[hrupp@pickeldi ~]$ jps
25870 Jps
26723 Main
25711 rhq-enterprise-agent-3.0.0.Beta1.jar
9353 Main
23340 Main
25839 AgentMain
[hrupp@pickeldi ~]$ jps
25918 Jps
26723 Main
25895 rhq-enterprise-agent-3.0.0.Beta1.jar
9353 Main
23340 Main
[hrupp@pickeldi ~]$ jps
26723 Main
26223 Jps
9353 Main
26196 rhq-enterprise-agent-3.0.0.Beta1.jar
23340 Main

So it connects to the server downloads the bits, does not manage to install them, connects again with the old version ...

Server log:

10:46:44,010 ERROR [[/]] AgentUpdateServlet: Failed to stream agent jar
java.lang.RuntimeException: Stream data cannot be copied
        at org.rhq.core.util.stream.StreamUtil.copy(StreamUtil.java:118)
        at org.rhq.enterprise.gui.agentupdate.AgentUpdateServlet.getDownload(AgentUpdateServlet.java:131)
        at org.rhq.enterprise.gui.agentupdate.AgentUpdateServlet.doGet(AgentUpdateServlet.java:94)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.rhq.helpers.rtfilter.filter.RtFilter.doFilter(RtFilter.java:124)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
        at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:182)
        at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
        at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:262)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:844)
        at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:446)
        at java.lang.Thread.run(Thread.java:619)
Caused by: ClientAbortException:  java.net.SocketException: Connection reset
        at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:358)
        at org.apache.tomcat.util.buf.ByteChunk.append(ByteChunk.java:354)
        at org.apache.catalina.connector.OutputBuffer.writeBytes(OutputBuffer.java:381)
        at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:370)
        at org.apache.catalina.connector.CoyoteOutputStream.write(CoyoteOutputStream.java:89)
        at org.rhq.core.util.stream.StreamUtil.copy(StreamUtil.java:112)
        ... 25 more
Caused by: java.net.SocketException: Connection reset
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:96)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
        at org.apache.coyote.http11.InternalOutputBuffer.realWriteBytes(InternalOutputBuffer.java:737)
        at org.apache.tomcat.util.buf.ByteChunk.flushBuffer(ByteChunk.java:434)
        at org.apache.tomcat.util.buf.ByteChunk.append(ByteChunk.java:349)
        at org.apache.coyote.http11.InternalOutputBuffer$OutputStreamOutputBuffer.doWrite(InternalOutputBuffer.java:761)
        at org.apache.coyote.http11.filters.IdentityOutputFilter.doWrite(IdentityOutputFilter.java:118)
        at org.apache.coyote.http11.InternalOutputBuffer.doWrite(InternalOutputBuffer.java:570)
        at org.apache.coyote.Response.doWrite(Response.java:560)
        at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:353)
        ... 30 more