Fixed details in antsRegistration interface

The generation of output filenames was incomplete for inverse outputs
in both collapsed and not-collapsed modes.

Additionally, collapsed mode for only-linear registrations was broken
as the warp file was not generated (but checked for existence)
Minor fix ensuring good values in output

invert_flags in collapse mode got unexpected values (not boolean)
for nonlinear transform
fixed treatment of filename when namesource is not a file
fixed mrtrix direction generator out file treatment. Depends on command
filename previous commit
set default option
trailing space is probably making travis fail in #798
test also for parameter based source name for output file
fixing command filename tests
Simplify input of a single LUT. Closes #726
Fixes for SPM ApplyTransform
Updated test for SPM ApplyTransform
Fixed bug with ants initialization

On one hand, invert_initial_moving_transform was used and needed to
be defined. On the other, as there is a xorg spec with initial_moving_transform_com,
it was still failing.
PEP8 formatting
Merge branch 'master' into bug/FixAntsInitialization
fix: updated prov model
fix: updated prov model to allow QNames
Revert some changes that broke file gathering, added more efficient
commandline creation.
fix: update location attribute
Added new workflow for doing recon all on skullstripped data.
Fixed doctest