Indexing Chapters 1-4

[schacon]

The start of finishing up the basic indexing work of Chapters 1-4

Closes #13; closes #14; closes #15.

[ben]

I went ahead and ran with this, the result is up on Atlas. Let me know if there's anything you hate about the way I did it. Basically, I added an index entry for:

• Any section heading (though these should be attached to the following paragraph, not the heading itself). People sometimes skip the TOC and go straight to the index.
• Any usage of a git command that adds information on how it works is indexed under git commands.
• Proper names get an entry if there's a whole sentence about them.
• Only one mention of a particular term per section or subsection. abcdef, 8, 8, 8 isn't very useful.

It might be overkill. Or it might be really useful. I'll let you be the judge.

[ben]

Fixed a couple of things: new PDF

[ben]

Merging for now, we can revisit later.