revisions to tools, warmup, readme, yet_more_tools

Tools:
* Sorry, the diff will be very hard to read because I moved the command line & git section below R and Python. (I moved it because it "felt" a bit too overwhelming at the top of the document once I added more links and explanation, and because I wanted to slightly deemphasize it versus spending prep time in R and Python.)
* Anyway, I added some new links and explanation of those links, plus some additional explanation of why we are learning command line and git.

Warmup:
* Revised second paragraph
* Added additional optional task

Readme:
* Added link to warmup

Yet_more_tools:
* Removed link that is now a duplicate with tools