Moved LSQ6, LSQ12 and NLIN protocol options to their corresponding option groups within the appropriate modules (e.g. LSQ6, LSQ12, NLIN). This resulted in minor changes to all four applications.

This will make it easier to implement the code necessary to address Issue #90.

As a result, I have deleted the paramsOptions class and all of its subclasses.

Updated help for --lsq12-max-pairs option, to indicate that it is not yet implemented. (Captured in Issue #93)
Moved registration method option to NLIN module options. Changed default from minctracc to mincANTS.
Merge branch 'opts-params-refactor' into develop