Help Understanding Template Hierarchy

Template hierarchy consist of templates, but not every template file is necessarily in hierarchy.

Essentially hierarchy determines entry points (one of matching templates with pre-defined name structure), but from there template can further load additional arbitrary files.

page-templates directory holds custom templates for pages (is_page() branch in hierarchy). It’s recent development that they can now reside in sub-folder.

content-*.php templates are called by Twenty Twelve like this from other templates: get_template_part( 'content', get_post_format() );. They are named arbitrarily and not part of template hierarchy – just a code organization choice that developers of this specific theme made.