ulyngs/oxforddown: Major & minor improvements (pandoc citations now used by default!) + bug fixes

This release marks a number of major and minor improvements.

• you can now use pandoc for citations, which causes less trouble than biblatex or natbib. Pandoc is used by default, but you can still manually opt-in to biblatex or natbib instead
• there is now only ONE template that is used both to knit the entire thesis and to knit individual chapters

• overflowing code in code blocks now line wraps!
• most non-essential parameters now have sensible fall-back defaults, such that the thesis still knits if the relevant variables are missing from the YAML header (this is what allows us to now use the same template to knit individual chapters with a minimal YAML header)

• the reference chapter now has correct running headings (this was temporarily broken when I added pandoc as an option to manage citations)
• many, many more tiny bug fixes..