Do not write out a new version of a model's source code when generating an OMEX file

[maxneal]

When writing a model to an OMEX archive, the original source code (AKA legacy code) should be written out, not an updated version produced by the SBMLwriter or CellMLwriter. We should also not allow the user to alter the reaction network structure of SBML models once imported into SemGen (i.e. by changing the sources/sinks/mediators on processes). If an SBML model's reaction network is altered, then a new version of the SBML code would have to be written out whenever the model was exported.