As I begin writing the make-metadata.R script, I'm not sure as to its purpose. Is it supposed to make my life easier by grabbing programmatically things like modification dates, MD5 sums, and such? (In which case it would only work on my machine, where I have access to the files locally.) Or should I simply write those things out by hand?

In short yes it is designed to make your life easier to programmatically make the inst/extdata/metadata.csv but it also allows us to review the metadata.csv file creation to ensure correctness. There should also be a make-Data script in inst/scripts that describes in R code and sudo code the generation of the data.