ulyngs/oxforddown: Stable release with bug fixes and minor new capabilities

As I've been finishing my own PhD thesis, I added a bunch of minor capabilities that were missing, and fixed a number of bugs. I've fixed enough of them now to warrant a new version number. Version 1.1 includes: ability to set from the YAML in index.Rmd whether or not hyperlinks should be highlighted in PDF output with a coloured box (I've turned this off by default, as I found it was too distracting to read when printing) ability to set set from the YAML in index.Rmd whether DOI's should be included in the bibliography a note that the chunk option fig.scap can be used for short figure captions in the List of Figures in PDF output numerous misc bug fixes Enjoy