Fixes example indentation of nested sections

We have to be very careful to never indent preformatted text in the DOM because the text itself will acquire that indent. There was a bug prior to this version where static & instance members of namespaces would be indented - this fixes that bug.

Updates for theme system 2.0.0

With the new theme system, themes aren't just folders of Handlebars templates - they're node modules with much more power. This updates the default theme to the new system.