Unspecialise application module

This PR unspecialises the application module by doing four things:
- Moves cache directory to root
- Moves logs directory to root
- Moves bootstrap.php to root
- Moves application module into modules directory

Making the application module just like any other has many benefits:
- The application module is completely optional, you could delete it and Kohana would still run just fine.
- It removes the need for APPPATH which means it can potentially be deprecated in the future.
- The bootstrap, cache and logs become uncoupled from Kohana modules/CFS so they can be more easily used with other libraries.
- It encourages users to split up their application into multiple modules instead of piling it all in application because they think it's special.

If everyone is in support of this change then I'll PR the changes needed to the other modules in order to make the build pass.