Updates to manual, and a few other tidbits

This request is primary for https://github.com/Toblerity/Shapely/issues/39 but also tidies up other aspects in the source tree. Each commit has a detailed list of changes. I didn't document any examples for ``affinity.affine_transform``, as I can only think up complicated examples. I was thinking about adding some "advanced" section at the end to explain how to combine a few operations, e.g. combine point.buffer() + scale + rotate to produce an oriented ellipse.

Note that the additions to the manual for affine transforms now includes math directives, which requires LaTeX and ``dvipng`` to build the HTML source. Alternatively, mathjax can be used to render the math via a modern browser instead, see ``docs/conf.py``.

Let me know if there is anything left that needs documenting (or if I need to undo any unwelcome changes).