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: Direct initialization for SyN registration process

This patch allows us to save the last state of the current registration to
the disk using the "save-state" option; then, it is possible to use the
"restore-state" option to load and restore the saved state later for the
direct initialization of the next registration process.

This patch should be built based on the following changes to ITK:
http://review.source.kitware.com/#/c/17729/
ENH: Improved organization and readability of write options

Added logic to better safegaurd users from mis-use of
the command line options.

When choosing to write composite transforms, do *NOT* write
the individual transform as well.  Choosing to write composite
transforms needs to be mutually exclusive from writing
individual transform files.  The reason is that the anticipated
behavior is different for these two options.

If writing the indiviual transforms, the user is required to know
that the existing initial-moving-transform needs to be incorporated
in the next "apply transform" step, so it is not included in the
writing process, (unless it was generated automatically with
geometry/centerofmass).  Composite transforms include the
initial-moving-transform implicitly.

This is further complicated by the new performance improvement
that initializes the current linear stage transform with the
previous stage output with implicit conversion.  This provides
performance improvements because there is only 1 linear transform
that needs to be used for computing jacobians/warping.
BUG: save-state transform should be cloned from the result transform
BUG: Change the state file to include syn internal transforms

Now, the state file is in composite transform format that includes
output linear transforms
+ SyN FixedToMiddle displacement field + SyN FixedToMiddle inverse displacement field
+ SyN MovingToMiddle displacement field + SyN MovingToMiddle inverse displacement field