Solver Handler needs clearer and/or better handling of vcml-backed SedML vs. sbml-backed SedML

[CodeByDrescher]

Currently, there are multiple sections of the solver handler code that pass around "null" values for SBML specific objects, when SedML references a VCML document rather than an SBML document.

This should be fixed in two ways:

1. nulls should not be passed around to represent a lack of SBML objects when VCML is being used. This makes it seem as though something went wrong, was masked, and is now proliferating through the code.
2. The sections of code that handle both SBML and VCML back code should be renamed / cleaned to show they are used for both SBML and VCML backed archives.