knitrby its author, Yihui Xie. There is also a knitr book covering the same ground in more detail.
Makefilesin the data-analysis pipeline, by Lincoln Mullen
xcode-select --install, or just try to use e.g.
gitfrom the terminal and have OS X prompt you to install the tools.
.texformat directly, but it is more useful to just have it available in the background for other tools to use. The MacTeX Distribution is the one to install for macOS.
pandoc-citeprocfor processing citations and bibliographies, and
pandoc-crossreffor producing cross-references and labels.
makewhat the steps are to create the pieces of a document or program. As you edit and change the various pieces, it automatically figures out which pieces need to be updated and recompiled, and issues the commands to do that. See Karl Broman’s Minimal Make for a short introduction. Make will be installed automatically with Apple’s developer tools.