OK with these options inside catalina.sh the applications now boot.
I can't seem to see the server in APM WebView.
What would the reasoning behind this?
I have the correct setup in the IntroscopeAgent.profile.
Are you talking about the application frontends? Do you see at least the servername? Does the problem occurs for Confluence and/or JIRA? if possible attach a screenshot
Open the agent logs, check if you see the agent is connecting to the EM - if possible attach the agent log and collector log
Also, check in the status console, maybe the agent is being denied (you would need to update the LB xml) or maybe a clamp has been reached (you would need to update apm-events-thresholds-config.xml)
Am I correct in saying that the agent should run with an application restart?
I see nothing in the logs at all so, the agent doesn't seem to be running.
Could you explain a bit more about "check in the status console, maybe the agent is being denied (you would need to update the LB xml) or maybe a clamp has been reached (you would need to update apm-events-thresholds-config.xml)"?
Yes, that is correct.
If you don't see any agent log then the agent it not active, you would need to review your startup script again, something is wrong.
I have attached a sample tomcat startup script + some custom pbds/pbl from our test confluence wiki enviornment ( confluence.pbd, confluence.pbl, lingotek.pbd, postgresql.pbd and setenv.sh)
If you cannot isolate the issue, I suggest you to open a support case.
It may be best to open a case to dig deeper into this should there be multiple issues needing addressing.