Fix some inaccuracies in Packaging.txt.md.

We still allow compiling against a different Nginx when natively packaged.

[ci:skip]
Require native packaging to specify the native packaging method
Introduce the buildout_dir locations.ini option in order to get rid of some dependencies on source_root
Make MessagePassingTest less timing sensitive
When Phusion Passenger is installed through the Debian package, passenger-install-apache2-module now checks whether the Apache module package (libapache2-mod-passenger) is properly installed, and installs it using apt-get if it's not installed.

Fixes issue #1031.