App guide: better integration, drop much incomplete content

Quite a bit of cleanup.

Things that could still use work before print edition, time permitting:
* Make Markdown in chapter 5 look more like HTML (ugh) as in other chapters
* More cross-references between Eric's content and mine
* Take a look at the tuning content in chapters 3 and 5 and make sure the same messages are being conveyed in each (and consider whether they should be merged)