[C++] have autodoc process handle subdirectories in the cpp source directory properly

[suntzu86]

After #353, the C++ autodoc pipeline (doxygen, sphinx, breathe) now captures the source files in the cpp/gpu directory but it does so by flattening out the gpu directory. Plus, the src dirs have to be hardcoded in docs/doxygen_config, docs/cpp_rst_maker.py, and docs/conf.py. This is less than optimal.

We should (as much as possible):

1. have autodoc tools pick up subdirs automatically. there should be a way to use wildcards in doxygen_config and conf to automate this. and we can similarly automatically build a list of all cpp src dirs in cpp_rst_maker.
2. modify cpp_rst_maker to construct separate 'modules' so that the C++ file documentation follows the same directory structure as the source code (instead of dumping everything into one huge docs page).