MAINT: add all source files to MANIFEST.in

sdist with setuptools doesn't play along with source files generated
from Numpy's templates, so they need to be included manually.
BUG: setup.py: pass non-prefixed scipy path to cythonize, but set cwd

This ensures cythonize.dat doesn't depend on cwd. This fixes the build
on pip when Cython is not installed.