Second check-in addressing Issues #83 and #84.

Continuation of commit ca5999a6e351, the following changes have been made:
1. Splitting of setMinctraccParams into two classes: a Nlin base class and a child LSQ12 class. NLIN is the base class because the linear parameters that may be specified are a subset of the total allowed parameters, and setParams handles this appropriately.
2. created a child ANTS class that reads in a single generation of ANTS parameters. This may turn into the base class as development proceeds.
3. Moved the setting of LSQ12 params out of the LSQ12.py module and into the setLSQ12MinctraccParams class, pursuant to point 1, above.
4. Added subject_matter as an argument for setting minctracc params (both LSQ12 and non-linear). This might be changed depending on how we handle Issue #88.