revisions to tools, warmup, readme, yet_more_tools

[justmarkham]

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

[justmarkham]

P.S. For future changes to course contents, I'll do smaller, more-focused commits... I know that's your style and is also easier to decipher!

[ajschumacher]

Looks good - thanks!