purl the chapters to make code reference documents

[lmiratrix]

It would be nice to have canonical code snippets for various things. The main ones would be how to do on-desktop parallel code (all the code together including the detect cores, etc). Right now we walk through code, but it makes it hard to cut and paste for on-line. How do we want to handle that?

Idea is to use purl to grab and make reference scripts for each chapter automatically. But we want to control which chunks are included. Perhaps we can have an code_reference = TRUE header value for the code chunks, and then purl could maybe subset to those chunks flagged for inclusion.

Or come up with some other idea for making such reference things---if we have only a few, perhaps doing by hand is alas the right way.

NOTE: reviewing comments on purl gives no obvious control other than level of comments kept. Perhaps looking at purl code would help. Or perhaps other packages exist.

[jepusto]

Looking through knitr::knit(), there doesn't seem to be a way to control whether or not specific code chunks are included when running purl(). But perhaps we could add a chunk option (e.g., purl = FALSE) when we want to omit a chunk, and then write our own post-processing function to tidy up the output after calling purl().

If we want to automate this for every chapter, then it's probably better to do so in a separate script that just walks through all of the .Rmd files in the repo, rather than trying to include it at the end of the source code for each chapter (i.e., let's not try to make the document purl itself when knitting).