Remove direct access checks

Issue: https://github.com/kohana/core/issues/508
@rjd22 This PR makes all classes and logs directly accessible to the public, that's the point. It will be followed by (or something similar) adding a 'web' directory in kohana/kohana which contains index.php and other public files. This way, all private files will be inaccessible by the web server if set up correctly.