We use preprocessed Java - that is, Java that contains macros to be processed. Currently ohcount (like sloccount) ignores these .jpp files.
The .jpp files contain our most significant code.
http://www.ohloh.net/p/vexi
This would fix the erroneous "C++ project" conclusion, and given our documentation in Java files being ~24%, the "poorly documented" warning should go away too.