This is a major release that simplifies how you build your thesis, adds useful functionality and fixes a number of bugs.

Major changes

To build the entire thesis, you now simply knit the index.Rmd file. You control the output format by commenting in or out the format you want in the YAML front matter.
The build function used by the knit button can easily be customised by editing the corresponding R script. This removes the use of make, which simplifies the build process and streamlines it across operating systems (make can be a pain on Windows)

New functionality & documentation

You can now hide or show line numbers by setting includeline-num to true or false in index.Rmd (thanks Ilse Pit!)
You can now switch between the biblatex and natbib LaTeX packages for handling references, by setting corresponding options in index.Rmd, and you can also pass some options to these packages directly from index.Rmd
The sample content now includes an example of how to include another paper in your thesis as an R Markdown child document
You can now easily customise or replace the title page, so that it is easy to tweak oxforddown for use with another university's front matter - a section on how to do this has been added to the documentation

The yaml options header_includes and in_header now works correctly (#17)
The fix for header_includes etc also means that kableExtra now correctly includes its latex dependencies automatically when the library is loaded, so many of its dependencies have been removed from the oxforddown latex templates (#14)
Fixed bug in hiding or showing hyperlink borders from index.Rmd (#18)
oxforddown now uses the MIT license