Instructions followed, you'll be glad to hear.
1) the agent is reporting to the controller - the getting started stays at "Waiting for connection", and doesn't go any further.
2) CATALINA_OPTS="$CATALINA_OPTS -javaagent:/home/ubuntu/appagent/javaagent.jar"
3) Tomcat version is
8.0.32-1ubuntu1.4
4) there is no logs directory, so no logs to send - the only thing I can send is the catalina.out containing the app agent information, which I included in the original, but here it is again (there is nothing else in the logs associated):
Full Agent Registration Info Resolver using selfService [true]
Full Agent Registration Info Resolver using selfService [true]
Full Agent Registration Info Resolver using application name [null]
Full Agent Registration Info Resolver using tier name [unknown]
Full Agent Registration Info Resolver using node name [null]
Install Directory resolved to[/home/ubuntu/appagent]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[DEBUG]: AgentInstallManager - Full Agent Registration Info Resolver is running
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Full Agent Registration Info Resolver using selfService [true]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Full Agent Registration Info Resolver using selfService [true]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Full Agent Registration Info Resolver using application name [null]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Full Agent Registration Info Resolver using tier name [null]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Full Agent Registration Info Resolver using node name [null]
log4j:WARN No appenders could be found for logger (com.singularity.SelfServiceNameResolver).
log4j:WARN Please initialize the log4j system properly.
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[DEBUG]: AgentInstallManager - Full Agent Registration Info Resolver finished running
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Agent runtime directory set to [/home/ubuntu/appagent/ver4.3.1.0]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: AgentInstallManager - Agent node directory set to [qa-003]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Using Java Agent Version [Server Agent v4.3.1.0 GA #15057 r867530f5c748a55ce75851534ad0942226c06d8b 45-4.3.1.next-analytics]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Running IBM Java Agent [No]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Java Agent Directory [/home/ubuntu/appagent/ver4.3.1.0]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Java Agent AppAgent directory [/home/ubuntu/appagent/ver4.3.1.0]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - ####################################################################################
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Java Agent Directory [/home/ubuntu/appagent/ver4.3.1.0]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Java Agent AppAgent directory [/home/ubuntu/appagent/ver4.3.1.0]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - Using Java Agent Version [Server Agent v4.3.1.0 GA #15057 r867530f5c748a55ce75851534ad0942226c06d8b 45-4.3.1.next-analytics]
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[INFO]: JavaAgent - All agent classes have been pre-loaded
[Thread-0] Thu Jun 22 11:00:57 UTC 2017[DEBUG]: JavaAgent - Using Java Version [JAVA_18] for AppDynamics Java Agent
Running obfuscated agent
Started AppDynamics Java Agent Successfully.
[Thread-0] Thu Jun 22 11:01:01 UTC 2017[INFO]: JavaAgent - Started AppDynamics Java Agent Successfully.
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