R1:5fd46dce663d

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out-of-date module definitions, and this limits that.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.

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