Hi,
We should be able to monitor any java based webapp as long as the target compiled classes are .class , Can you define POJO rules on Clojure classes and see if that helps?
https://docs.appdynamics.com/display/PRO41/POJO+Entry+Points
In some cases, we might not auto discover BTs could be due to that we are hitting out of box supported entry points like servle, struts, JMS etc and we could still continue to define custom pojo rules on target class and monitor as BT