JTransc has a maven plugin that hooks the package maven phase and transcompiles all the code into the target app. Since you can call maven from console I just wanted to debug easily on intelliJ. It ended being pretty easy.
Instead of calling mvn command, there is a mvnDebug command:
mvnDebug package
It will be waiting, listening to port 8000 by default.
In intelliJ you must create a Remote run configuration, and just have to change the port to 8000. While mvnDebug is waiting you can execute the run configuration. And breakpoints should just work, if you have the sources of the plugin.