Add knitr option for path

[pattyf]

Add
knitr::opts_knit$set(root.dir = normalizePath('../'))
to the knitr setup options for the Rmd files for pt2 & 3 (done for pt1) so that the Rmd files can knit in the docs directory but reference the data files from the root directory in any R chunks.

Note: The images directory was moved under docs because it is only used in the Rmarkdown files and the relative path setting only works for chunks (not markdown).