With Puppet 3, we call the initialize_global_settings method with the --confdir and the value of the :puppetconfdir setting. However if the puppet.conf references $vardir (which settings do by default) then --vardir also has to be set when we initialise Puppet.

As mentioned in Jeff's comment here, this had to be added to the puppet config.ru for 3.0.1 too:
http://projects.puppetlabs.com/issues/16637#note-9

This is equivalent to how we initialise Puppet 3 today, which throws an error:

irb(main):001:0> require 'puppet'
=> true
irb(main):002:0> Puppet.settings.initialize_global_settings(['--confdir', '/etc/puppet', '--run_mode', 'master'])
=> true
irb(main):003:0> puts Puppet[:hostcert]
Puppet::Settings::InterpolationError: Error converting value for param 'hostcert': Error converting value for param 'certdir': Error converting value for param 'ssldir': Could not find value for $vardir

1. :puppetconfdir is actually pointing to /etc/puppet/puppet.conf usually, so this should really be --conf rather than confdir
2. :puppetconfdir was removed in 7c08e30a47a16d387f26d1c617cdedc60d9d0582
3. missing comma in my commit inside '--run_mode' 'master'