Since CKEditor 4.3.3 release (In-Portal 2.x uses CKEditor 3.6.3, In-Portal 3.x uses CKEditor 4.2) it's also available for usage through Composer (see http://ckeditor.com/blog/CKEditor-Supports-Bower-and-Composer).
We can use this to our advantage and only keep our custom CKEditor plugins/config in the core/ckeditor folder.