3.4/develop

This pull request is in relation to my other pull request for kohana/kohana: https://github.com/kohana/kohana/pull/27

Kohana::modules() now loads modules in order instead of bottom to top. This really confused me when I first began using Kohana and I'm sure everyone would agree this is much more intuitive (for a programmer at least).

Modules are now enabled explicitly in the bootstrap instead of magically being added in the core. This gives the user greater control, and helps them understand what's really going on instead of lying to them. For example, you can now run Kohana without the application module if you wanted.

Kohana::$_paths was removed and replaced with Kohana::$_modules. The only difference between the two was that $_paths had numeric keys instead of the module names therefore it wasn't needed.