STYLE: Further comment out dead code

The collapse-linear-transforms-to-fixed-image-header option is
currently not supported.  It will also be removed from niype interface.
ENH: Add command line robustness feature.

Previously if an erroneous command line flag was given (i.e.
--silly-wont-work-flag) the program would silently ignore that flag
and continue to run.  This was problematic because if you accidently
had a typo in the command line option, it was very hard to determine
that that flag was not being used.
Merge pull request #126 from BRAINSia/ImproveCommandLineProcessing

Improve command line processing
WIP: add displacement field output
ENH: antsMotionCorr 4D output
WIP: replicate displacement in ImageMath
ENH: replicate displacement in ImageMath
ENH: replicate image in ImageMath
BUG: antsMotionCorr.cxx:1384: warning: array subscript is above array bounds
ENH: allow optional double precision registration
BUG: parse check on 0 name

Was too agressive. Checking 0 named entries. Causing failure for antsSliceRegularizedRegistration
This latter example needs a test
ENH: interpolation
ENH:  Add additional check for registration quality.
BUG:  LABELS not IMAGE.
ENH: Add diagnostic information.
BUG: forgot invtx interpolator
COMP:  Initialize index.
DOC:  Improve documentation.
BUG:  Don't use quotes.
BUG:  Better bash comparison.