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.
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.