Hello Colm,
Several issues that have been reported when configuring the agent with confluence and JIRA.
For Confluence, I suggest you to try the below settings:
..
CATALINA_OPTS="-javaagent:<wily_home>/Agent.jar ${CATALINA_OPTS}"
CATALINA_OPTS="-Dcom.wily.introscope.agentProfile=<wily_home>/core/config/IntroscopeAgent.profile ${CATALINA_OPTS}"
CATALINA_OPTS="-Datlassian.org.osgi.framework.bootdelegation=com.wily,com.wily.*,sun.*,org.w3c.*,org.xml.sax.*,org.apache.xerces.*,com.sun.org.apache.xalan.*, org.apache.xml,org.apache.xml.*,javax.xml,javax.xml.*,com.sun,com.sun.*org.apache.xalan,org.apache.xalan.* ${CATALINA_OPTS}"
CATALINA_OPTS="-Djavax.xml.parsers.DocumentBuilderFactory=org.apache.xerces.jaxp.DocumentBuilderFactoryImpl ${CATALINA_OPTS}"
CATALINA_OPTS="-Djavax.xml.transform.TransformerFactory=org.apache.xalan.processor.TransformerFactoryImpl ${CATALINA_OPTS}"
For JIRA, you can try a similiar set of settings, it should work most of the time, but you see exception when using for example the JIRA Configuration Manager (xml import).
There is an enhancement request to have APM supported with all Attlassian products:
I hope this helps,
Regards,
Sergio