applywarp --usesqform will currently fail if the input or reference image qform and sforms are not equivalent to within a strict tolerance. applywarp will currently also always use the sform, regardless of the sform/qform code values. This MR removes the equivalence restriction, and changes applywarp to use the sform or qform, depending on their codes.
There is no reason for a tool to require that the sform and qform affines are identical. All tools should follow the standard FSL convention of using sform if sform code !=0, or qform if qform code !=0, or a fall back scaling affine.