matlab folder clean up

Removed all matlab code files that were deprecated or relocated to
private repo.
Resolved issue #71 by changing the location of the file creation to correct test directory.
Merge branch 'master' of https://github.com/campreilly/UnderSeaModelingLibrary
Reformat of line, test commit.
Resolved issue #73, no valgrind error/warnings are produced for ray_speed, and the warnings produced from the usml_test/datagrid_test suite have been addressed. Additional comments were added at the beginning of the test suite outlining these warnings.
Added run_id to @param list for constructor, issue #72 has no other errors produced. Various warnings are issued from the Doxyfile and may need/choose to be updated to resolve these warnings.
Removed extra constructor in reflect_loss_rayleigh and address issue #51. All tests produce results that are the same as in Jensen and Kuperman.
Part of deprecated code that was to be removed was missed.
Removed deprecated code.
Move matlab test routines for studies into the
appropriate subdirectory of usml/studies.
Remove old copies of analytic_wedge matlab scripts
from waveq3d/test directory.
Remove out-of-date copies of demo GUI.
* Update CMake process
  -- Read version number from config/VERSION.txt
  -- Increase min optimazation level to -O1 and add warning not to
     use -O0 option.
  -- Re-enable used of FindBoost, add support for 1.56 and 1.57 versions
  -- Use ${NETCDF_INCLUDES} to find ncks instead of hardcoding
  -- Move usmlBuildStudies.cmake and usmlBuildTest.cmake to config dir
  -- Remove Boost_FORCE_SHAREDLIB option, no longer used
  -- Remove USML_SAFE_BESSEL option, will hardcode where used.
  -- Remove  GPROF_PROFILER option, not needed by valgrind
  -- Move all Additions logic to the end.

* Update make_tar.sh proccess
  -- Read version number from config/VERSION.txt
  -- Move script to config directory and allow it to locate itself.
  -- Automatically run doxugen if html directory missing
  -- Write outputs to ../usml-delivery insteal of ..
  -- Add delivery of *.pdf reports used on web site.
  -- Update usml_frontpage.html for version 1.0.0
Updated RPM creation routines provided by Ted.
Removed older versions.
rename make_tar.sh to delivery_src.sh
add breif option to only build soiurce tar ball
Move RPM generation into library of LVCMS specific routines.
Change deliver_src.sh back to its original name, make_tar.sh
Update install materials.
Change default for USML_PEDANTIC and USML_BUILD_STUDIES to OFF.