Added classes so that the appropriate option groups are now included in minc_parameters.py.

The command line options for --lsq6-protocol, --lsq12-protocol, and --nlin-protocol were moved here, and a series of classes were written to handle adding these options to the option groups in different modules.

As such, these options were removed (as written) from the LSQ6, LSQ12 and NLIN modules and re-added using the new framework. All were added to MBM.

Other minor changes:
1. Removed Matthijs' clever code for the epilogue, since we reference example protocols in the help for each option. (And will in the documentation as well.)
2. Fixed a bug in LSQ12 with the w_translations array--sloppy copy and paste, too many parameters!
3. Moved --calc-stats option to stats module.
4. Re-organized order of MBM options.