Further clean up

[gavinsimpson]

Additional cleaning up required:

• The figure-generating chunks were renamed prior to submission but the figures were not rendered or committed
• Deleted the now obsolete versions of the figures
• Updated Makefile to include an make R option to purl() the .Rmd into an .R script.
• Included Neotoma_paper.R, the purl()ed version of the .Rmd
• Configure knitr via the .Rmd to use a single cache for the document rather than separate caches for each format.

I think we are now pretty much clean; except for deleting .Rproj the main repo is clean and we can decide if we want to retain the misc/ folder later.