Cleanup doxygen file
- Use "doxygen -u" to clean up incompatible options
- Exclude netcdf/msvc from doxygen
- Remove @todo issue from reflection model.
- Update doc on wave_front::find_edges() to reflect current implementation.
- Update doc on wave_queue::init_netcdf() to include
  upper_vertex, lower_vertex, and on_edge in example.
- Remove use of pTargets_sin_theta and boundary_check from
  wave_queue::wave_queue() constructor.
Merge branch 'master' of https://github.com/campreilly/UnderSeaModelingLibrary
Search and replace all instances of unsigned with size_t.
-- Test by compiling under Linux 64, Win32, and Win64.
-- Win64 found the most errors because their "size_t" is not a "long".
-- Required modifying NetCDF-3 C++ interface to resolve issues on Win66.