STYLE:  Remove unnecessary string conversion

Removed unnecessary string conversion to
character array that may cause problem for really long
paths.
ENH: Add 2D branded image writing for QC purposes.
BUG: BCD was applying the inital transform 2x

ENH: Modularize and re-use common code as functions.
ENH: First computational enhancement using std::inner_product
ENH: Make test suite more verbose in outputs for easier validation.
ENH:  Implement Atlas based final adjustment

BCD now has an option to finalize the alignment against
a template image.  with a shifting of the ACPOINT back
to zero.

This involved some major refactoring and renaming of
variables to make it easier to read, and better
describe the behaviors.