Parse OMEX files with multiple SED-ML files not marked 'master'

[luciansmith]

The 'standard' way to package up the SBML Test Suite models is to give them a bunch of SED-ML files (one per SBML level/version) and just flag the latest level/version as 'master'. This seems to confuse VCell's OMEX interpreter.

https://biosimulations.org/runs/689388c01113c21d848f36a7#tab=log

vs.

https://biosimulations.org/runs/68938d3c1113c21d848f3d05#tab=log

[CodeByDrescher]

It looks like for whatever reason, the VCell BioSimulator's status log decided to record each instance of SedML in the archive, despite knowing that only the master marked file should be run.