Improve part 3

- Can't start mysqld as peon, but it has to be running before invoking
  bin/storage upgrade. So I just replaced those commands with a comment.
- Fixed rewrite rule in nginx conf block. This is the rewrite rule that
  Phabricator's configuration guide uses. I was experimenting with a
  different rule, but I'm not sure it works 100% of the time.
- Broken link to the FQDN part. Partway through my editing, I swapped
  part 4 (which was SSL) with part 5 (which was domain names). Looks
  like I forgot to fix this link.
- Clean up the command to set the repo root. This was kinda poorly
  phrased, and long inline code tends to wrap at the wrong places.