Added Advagg default settings to bear_habitat_prod, removed advagg from dependencies on bear normal install. Still gets added in the make file during installation in case bear_habitat_prod is enabled.

Added media_wysiwyg dependency back to fix issue with ckeditor and media, added a core patch for file uploads

Updated main readme and added patches folder with all patches from current make file. Included a readme there also.

Updated entity and entity reference for security, added patch to fix template_preprocess_entity issue http://drupal.org/node/2003826.