yes there is a dedicated way to do it, unfortunetaly it seems there is some issue with it :
when you select one of your java project (which have dependencies to other of your projects), on "java and inventory model discoverer" parameters screen, you may click on "ELEMENTS_TO_ANALYZE" button and select not only one but several projects among dependencies to reverse to one single jav2kdm model.
After some basic tests, i observe some "IllegalArgumentException: No Null constraint". This multi-project selection works fine with simple java model discoverer. I think there is some issue in kdm model mapping with directories in several workspace projects.
I will feed some bugzilla about it.