More updates, including to the build system.

* Fixed CMake system so that everything will build on Ubuntu as well as Windows.
* Mild fixes to the python documentation generator to talk about 'sbml2matlab' instead of Antimony
* Better python install system for Windows
* Removed a ton of commented-out code from NOM.
* Made NOM leak less and take const char*'s in places where they were needed.
* Now return matlab code that is nothing but a comment on the error in the SBML document, if there was an error.
* Don't error out on SBML warnings.
* Don't produce "1.NAN" or whatever if the SBML didn't have a value set--now default everything to 0.
* Properly delete things that should be deleted, and free things that should be freed.
* Properly initialize values of sbml2matlab classes, so they can be deleted without fear (also, delete them).
* Change odd behavior of sbml2matlab.exe where it was called with a single argument:  it used to assume that the single argument was actual SBML; now it assumes that it is an SBML file.
* Generally clean up 'main'.