#445830: Follow-up to Rename clear-block CSS class to clearfix because I missed a few clear-block classes

Renamed #navbar div to #navigation, $navbar region to $navigation, .with-navbar class to .with-navigation and added #navigation .section div

- Added $classes and $classes_array to all templates, not just Zen's templates.
- Renamed page.tpl's $body_classes and $body_classes_array to $classes and $classes_array
- #564068: Views classes are missing from $classes variable

#317417 by JohnAlbin and quicksketch: Fix off-line maintenance page since drupal_get_path('theme', 'zen') won't work

#375953: follow-up, change sidebar primary/secondary to first/second to match proposed D7 region names.