AFNI enhancements & doctests

@chrisfilo, @satra, @hjmjohnson,

Added 3dDeconvolve() and Zeropad(), more traited flags to Allineate() and others, updated style to conform better with PEP8 (http://www.python.org/dev/peps/pep-0008/) and increased doctest usage.

The doctest usage may or may not conflict with the web documentation style.  If so, I can move the offending tests to a doctest file, but I'll need help integrating that into the Nipype testing infrastructure.

Cheers, 
@dmwelch