Clean up the repo

This PR incorporates a large set of commits with the aim of cleaning up the repo.

This had to be rebased today following #34 but most of the commits today are just due to that rebase.

There are a couple more things needed to clean up fully, but we can do that incrementally later; main thing is to drop the `.Rproj` file from the repo (but others may want to keep these locally), and see if there is a way to have **rmarkdown** use a common cache for the different formats and a common location for files generated during rendering - i.e. the figures. At the moment, the `Makefile` results in separate cache and intermediate files folders for each document type.

However, suggest we merge this ASAP and then solve those minor issues after we tag the repo to mark the submission.