Improve performance by using Cython classes and functions

Turns PyStanHolder and PyStanArgs into Cython extension classes. Chains are now
wrapped directly using PyArray_SimpleNewFromData. Substantial speed improvements
derived from rewriting get_kept_samples and get_samples in Cython.
stanfit4model.pyx needs numpy libraries to compile

Add ``np.get_include()`` to include_dirs
Merge branch 'feature/pystanholder-refactor-alt' into develop