Allow specification of knitr options

Also included an `auto_figure_prefix` option that will configure
`fig.path` based on the file name, putting the result within
figure/

There's a tension here because doing too much within maker will
make the standalone knitr files less self contained.  But a similar
thing happens with running md files through pandoc etc; the formatting
is done there.  Most of the knitr options (changing figure format, size,
etc) are more akin to these options so it's going to be useful to
change them from outside of the document itself.  This means that a
single knitr document could produce a number of format outputs.
Updated the documentation to catch up with the package.