Fourth check-in addressing Issue #83.

Modified LSQ6 module to use new classes for setting parameters.

Major change: Created setLSQ6MinctraccParams and modified LSQ6HierarchicalMinctracc accordingly to use this class, removing duplicate code. setHierarchyOptions and setInitialMinctraccTransform no longer needed.
Related: Added self.fileRes to LSQ6Base for use in parameter setting. getFinestResolution now called only once. Renamed some parameters for consistency with other modules (necessary when using setLSQ6MinctraccParams).

Many minor changes:
1. Renamed lsq12_example_protocol to minctracc_example_linear_protocol since it can be used for LSQ6 and LSQ12.
2. Reordered nlin_protocol so optimization is listed last.
3. Updated help in LSQ6, 12 and NLIN modules to point to example .csv files. Updated general minc_parameters.py help.
4. Removed subject_matter from setNLINMinctraccParams, because it is unnecessary at this point. (This also allowed for cleaner design when adding initial_transform to setLSQ6MinctraccParams.) Again, may revisit this when we handle Issue #88.
5. Fixed bug so that simplex is now converted to a float instead of an int.