Explicitly enable application and core modules

The application and core modules must now be explicitly set in the bootstrap.php instead of magically being added in the core behind the scenes. This gives the user total control and flexibility over modules and makes all modules optional.

Kohana::include_paths() method has been removed, the only difference between this and Kohana::modules() is that it included the application and core module paths. Now that these two modules are included in Kohana::$_modules there's no need for the method to exist, likewise with Kohana::$_paths.

In the refactor of Kohana::modules(), array_reverse() is used before setting and getting modules. This makes it so Kohana::$_modules internally stores modules in the correct order, however externally it works in the same "top to bottom" fashion. As array_reverse() is now in one place, other methods such as find_file() don't have to worry about reversing the modules array before use.
Yes they do - I think @shadowhand meant to link to kohana/kohana#29 - the array access syntax here requires PHP5.4, but aren't based on a branch where that dependency has been updated.