Improve order of operations in upgrade script

Summary:

• Run "phd stop" before stopping apache. This is essentially a smoke test for

PHABRICATOR_ENV being set.

• Run documentation generation after everything else. Between the pull and the

restart we have some minor exposure to APC issues with deleted files and
out-of-date module definitions, and this limits that.

• Pull commands out of (x && y) stuff, this prevents "set -e" from working

correctly.

Test Plan: Ran upgrade script locally.

Reviewers: btrahan, jungejason

Reviewed By: btrahan

CC: aran

Differential Revision: https://secure.phabricator.com/D1419