Make the entire `Reference` class private

[sappelhoff]

https://pyprep.readthedocs.io/en/latest/generated/pyprep.Reference.html#

From my point of view, users should call pyprep.PrepPipeline(...).fit(), which then calls the Reference class and its methods in the correct order.

Please respond here if you think this class should remain public, and why.

[sappelhoff]

This would clash with:

• https://github.com/sappelhoff/pyprep/issues/73
• https://github.com/sappelhoff/pyprep/pull/99