BUG: Fixed final transform, updated the resampled output volume and other outputs accordingly
ENH: fixed all failing tests except acLowerBound, added translation of AC to origin as final step if atlas-registration mode is used.
STYLE: Code review of Ipek BCD changes

Removed dead code comments,  Removed debugging file writing,
Re-organized code to be more compact failure logic, fixed ITK style issues
Identified several places that need further investigation.
BUG: Removed aliased variables that were used inconsistently.
STYLE: Conform to ITK style.
ENH: When copying transforms, both FixedParameters and Parameters must be set.
ENH: Step 1 in decoupling outputs from transform estimation.
ENH: Remove duplicate functions, decouple outputs.

Some functions were duplicated in multiple compilation units.
Further work was done to decouple outputs from detectors.
ENH: Make function const correct

TransformResample does not modify the transform, so it should be
a const pointer.
ENH: Refactoring to modularize transform estimation

Put the complete transform estimations into the main class.
STYLE:  Removed deprecated LandmarkPaired.

The code for dealing with LandmarkPaird is now
isolated to it's own program.
PERF: Improved performance of BCD by minimizing work to be done.
BUG: Fix ACLowerBound test failure by passing proper image back to be written.
ENH: Update NIPYPE for new version of BCD.