1. save your project as XML, note that currently it doesn't handle external files so you have to pull everything into one
2. run RunRB2Doxy and File - Open that project XML file
3. choose Transform -> File and select a new .java filename
4. run Doxygen over the directory containing your newly created .java file

Note: there is a basic summary in the AAREADME file showing the command-line options for running the XSLT transformation using a Java processor. This is still possible but a bit out of date as I added the RunRB2Doxy project. It is convenient for people setting up batch processes.