3.4/develop

This pull request is in relation to my other pull request: https://github.com/kohana/core/pull/509
This pull request passes all unit tests.

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Fully embraced the composer way of doing things, everything must now be installed using composer including the core module and 3rd party modules.

Added requirement of PHP 5.4+ and changed all arrays to use the new short syntax.

The cache and log directories were moved out of the application module; there definitely shouldn't be directories with dynamically generated content inside a module.

The core and application modules are now explicitly enabled in Kohana::modules() which gives users complete control over what modules they want to use.

The bootstrap file has been merged into index.php. There's no need for a speperate bootstrap file since everything in index.php is application specific code too (and if not, it will be moved out of there in future updates).

The default routes have been moved to an init.php file in the application module (just like how every other module adds routes).

Since the application module doesn't now have any special circumstances, it can be moved alongside other user created modules in the 'modules' directory. It also means that the application module is completely optional and Kohana can run fine without it enabled.