Fix Makefile.nestedvm so that it works with make -j.

Instead of repeatedly reusing the file name 'PuzzleEngine.class' in
the main build directory, now each puzzle's NestedVM translation is
left in a separate subdirectory so that they don't collide with each
other. A bonus is that we don't have to rename the file back and forth
between the rule that builds it and the one that consumes it.