In MDL-50346 sub-directories in templates were allowed and theme/upgrade.txt was updated.  However it contains inaccurate information as:

The following are all valid template names and locations in your theme:
  theme_themename/columns2: theme/[themename]/columns2.mustache
  theme_themename/local/layouts/columns2: theme/[themename]/local/layouts/columns2.mustache

The following are core templates, locations, and override locations in your theme:
  core/modal: lib/templates/modal.mustache => theme/[themename]/core/modal.mustache
 mod_forum/forum_post: mod/forum/templates/forum_post.mustache => theme/[themename]/mod_forum/forum_post.mustache
  mod_forum/local/post/user: mod/forum/templates/local/post/user.mustache => theme/[themename]/mod_forum/local/post/user.mustache

should have the 'templates' sub-folder and therefore be:

The following are all valid template names and locations in your theme:
  theme_themename/columns2: theme/[themename]/templates/columns2.mustache
  theme_themename/local/layouts/columns2: theme/[themename]/templates/local/layouts/columns2.mustache

The following are core templates, locations, and override locations in your theme:
  core/modal: lib/templates/modal.mustache => theme/[themename]/templates/core/modal.mustache
  mod_forum/forum_post: mod/forum/templates/forum_post.mustache => theme/[themename]/templates/mod_forum/forum_post.mustache
  mod_forum/local/post/user: mod/forum/templates/local/post/user.mustache => theme/[themename]/templates/mod_forum/local/post/user.mustache