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Q1: I haven't tried using the gpu module, but it looks like it's in the header generator list (see modules/java/generator/rst_parser.py).
A decent debug strategy is to track the progress of the CMake build script at modules/java/CMakeLists.txt. For example, you can get a list of headers the system tries to parse by adding the line
message(STATUS "module_headers = ${module_headers}")
immediately after line 58 of modules/java/CMakeLists.txt.
Please let me know if you get stuck or need more explanation.
Q2: I'm not currently working on extending the Java wrapper, but there is ongoing effort by Hilton Bristow to make a Matlab wrapper. Work he does to improve the header parser, eg gpu header parsing, will automatically translate to the Java wrapper.