ENH: Add the linear transforms direct initialization flag to command line

A new command line, called "initialize-linear-transforms-per-stage", is
added that allows the direct initialization of the current linear stage
transform from the previous stage's linear transform; this allows
multiple linear stages to be run where each stage directly updates the
estimated linear transform from the previous stage.
(e.g. Translation -> Rigid -> Affine).
ENH: Make the collapsed transform keep the center of rotation

Previously the collapsed linear affine transform had fixed parameters
as all zero. Now we find the last transform that has a center, and set
that as the fixed parameters of the total transform, and it is done only
once.
If you wish to set the center explicitly, set before Offset computations
are done.  To define an affine transform, you must set the matrix, center,
and translation OR the matrix and offset