Remove direct access checks

Issue: https://github.com/kohana/core/issues/508
@lenton disagree. This PR should be merged ASAP or we're just storing up merge conflicts. 

Moving the kohana/kohana document root down to 'web' by default needs to be a separate discussion. I'm in favour, but it's been discussed before and there were valid reasons not to (essentially that we wanted to cater to people who just drop the whole project on a shared host, who may not be able/aware to make it so "all private files will be inaccessible by the web server if set up correctly").