Please see the README in bundles/org.eclipse.wst.jsdt.debug.nashorn for a brief description of the design ideas and a simple test case. The code is nothing but a spike and absolutely unpolished - I'd be very happy to get some feedback from the project team before proceeding any further on what might be the wrong track.
Somehow it feels like JDT is hiding a lot of JDI APIs I'd like to use, but this may be just my lack of expertise with JDT. At any rate, all the x-friends package exports both in JDT and jsdt.debug.core seem to be a bit of a code smell.
Next thing I'll try upgrading to Mars M6 and take a look at the JDT patch for the line location issue (bugzilla 462932).