A series of upgrades and changes have left instances with 'role::puppetmaster::standalone' applied in a broken state. This is unfortunate because Puppet is unable to fix itself. There is a small manual update required.
On the project specific puppet master (instance with role::puppetmaster:;standalone applied):
0. Make sure your copy of the operation puppet repo is current at /var/lib/git/operations/puppet
1. edit /etc/puppet/puppet.conf to replace 'default_manifest = $confdir/manifests/site.pp' with 'default_manifest = $confdir/manifests/'
2. restart apache (service apache2 restart)
3. puppet agent --test