fix the manifest modification * file descriptor leak * was not working if MANIFEST was not available.
pep8 and flakes
use consistently os.path.join in setup.py
rework the Extension part to be explicit instead of "black magic" :)

use also the cythonize method instead of importing the Cython Extension.
This is the recommended way from the cython documentation
just a reorganisation to put all setup.py methodes in the right section