Remove modindex from PDF contents

... as we do not have any module index page.

 http://book.cakephp.org/2.0/en/modindex.html
 http://book.cakephp.org/2.0/en/py-modindex.html

Like this one:
http://sphinx-doc.org/py-modindex.html
https://github.com/sphinx-doc/sphinx/blame/master/doc/contents.rst#L36

Partially relevant: https://github.com/cakephp/docs/issues/2068