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Of course you can debug custom adapter in Jdeveloper.
All you need is:
1) add "oai.jar" to your project libraries (if your full path to it is very long, JDeveloper can not see it - there is a bug, so you can simply place a copy of oai.jar near the root of your drive to make pathh to it shorter)
2) Paths -> Additional Classpath - take it from parameter service_classpath in adapter.ini
3) Runner -> Run Directory - directory where your adapter is located (where adapter.ini)
4) Runner -> Default Run Target - oai.jar\oracle\oai\agent\service\AgentService.class
P.S. you can additionally add adapter.ini in your project and edit it right here!