Fragment file generation

[trudack]

The commands to generate the fragment file so far works.

I would add an option to give the outputfile name and then move the rosetta outputfile name to something like

outname.frag9 outname.frag3 outname_rosetta.fasta

We will check how to specify fragment file prediction just for loop regions and provide @ryanmcgreevy with the commands that it can be added.

[ryanmcgreevy]

There is now a -o option to set a naming prefix for the fragment files (this uses the fragment picker's existing -out:file:frag_prefix option), and will take the name from the input fasta as a default.