Gapfills should always start from the same base model

[mmundy42]

As discussed at 6/29 meeting, GapfillModel() should always start from a model without other gap fills integrated. This makes each gap fill (say on different media) start from the same base model. For example, if a user submitted 5 gap fills on 5 different media it wouldn't make any difference if one of the gap fills completed before another gap fill started.

One thing we didn't discuss is how to handle model edits. Should model edits be integrated into the model before running a gap fill?

Implementing this change is a little tricky. When a model is retrieved using the get_objects() method in PATRICStore, the transform_model_from_ws() method() is called implicitly. The transform_model_from_ws() method always processes gapfilling objects that it finds in the workspace. Should we add a new option to get_objects() to control how a model is transformed? The option would then have to passed through to all of the transform_XXX methods that are defined.