Added more of the logic for merging files

Added all of the FASTA logic, and a good chunk of the GFF logic.

Unfortunately, I can't get to the point where we are displaying the errors until at least the prototypes of the mergeGff function are uploaded. This means that if it is not uploaded some time this afternoon, someone else may need to take over the responsibilities, as I am not available tomorrow.

I also took the liberty of making the tests not be broken, as it was causing Eclipse to complain at me.