As of 2011-11-01, most files in Drupal core live in a 'core' subdirectory. We did this to make it easier to tell what's core vs. site-specific code (e.g. to discourage people from installing modules into the 'modules' subdirectory in the webroot) and to make it easier to upgrade to newer versions. See #22336: Move all core Drupal files under a /core folder to improve usability and upgrades for the full story and/or the API change record: Most Drupal core files now live in a "core" subdirectory.
One of the only drawbacks of this change is that bug fix patches for Drupal 7 no longer apply to Drupal 8 without being rerolled. However, generally it's easy re-roll a patch in this situation. xjm wrote up detailed instructions for re-rolling patches here: http://xjm.drupalgardens.com/blog/rerolling-drupal-8-core-patches
Please don't reopen the original issue with follow-up suggestions or bug reports -- those belong in new issues.