Update index.php and Application\Module to make composer use optional

Update index.php and Application\Module to make composer use optional

- index.php now supports ZF2_PATH env var or git submodule
- re-add the git submodule to make non-composer install easier
- update the readme
- use include instead of include_once, see:
http://robert.accettura.com/blog/2011/06/11/phps-include_once-is-insanely-expensive/

If you are not using composer, you no longer have to make changes to the default
skeleton.