Change default transform type to affine in Registrator class

The default transform type, similarity, was giving strange
behaviour when more than two patches were selected to register the
images. In some cases, it appears that one of the points would be
ignored.

The reason for this behaviour is not clear but could be due to the
estimation method used in scikit-image.transform.estimate_transform
and how it regularises unstable points.
Ensure PEP8 compliance
Make docstrings accurate.
Refine CLI semantics and docstring

Make sure that the docstring used for docopt makes sense and
that all of the options are interpreted correctly.
Add basic documentation and usage to the README.rst

Incorporate very basic usage/workflow outline, including a brief
overview of how to make things happend.

Add some basic tips and tricks for possible use cases.
Incorporate MANIFEST.in

Make sure that the readme and the licence file is included in the
package.