Don't commit Sphinx build artifacts

The _build directory is where Sphinx puts the html, pdf, and other files after
building the documentation. These should not be commited.
Fixed build errors and warnings in userguide

These changes are to fix issues which were emitting errors and warnings during
the Sphinx build of the userguide.

In particular, adding a second underscore to the end of a hyperlink makes it
an anonymous hyperlink reference. This means that Sphinx won't keep track of
the hyperlink reference name and therefore not complain when more than one
hyperlink has the same link text (which it would do otherwize even though the
actual URL is different).