update merge utility and add trimming as an option

[marybarker]

Updates in this branch include:

• Added trimming option to the merge utility function, so that the result of merging protobufs together can be trimmed before saving
• The routine `TrimToMinWeight' no longer returns a single tree, but rather the DAG consisting of all of the min-weight trees in the original DAG.
• Misc small debugging for the case of missing data in the viral_dataset_snake file
• Option added to `larch-usher' for trimming the final optimized DAG