Remove organizations from the hierarchy.

Installation of Extensions is distinct from provisioning of an Extension
as a Resource.

An application's $APPDIR/resources.json controls what extensions are provisioned,
under what URLs, with what configuration.

bin/liveoak, if passed a path (including '.') will deploy that path as an application
named after the tail directory name when launching liveoak.

Update mongo configuration options to cover most of the mongo client options.
Now supports replica sets, mongo based security, default write concerns, read perferences, etc.