Misc changes and code clean-up:
1. Renamed --target option in LSQ6 module to --lsq6-target for clarity.
2. Added --lsq12-likefile option for resampling and updated both MBM and LSQ12 files accordingly.
3. Added a new nlin group to input file handlers prior to starting NLIN registration. This is consistent with additions of previous groups and makes output xfm names clearer.