Incorporate ideas from kohana-projecttemplate

* Move index and .htaccess to httpdocs folder - always use this as docroot
* Move modules, init and routes out of bootstrap.php
* Allow extra configuration per environment
  - This can also be used for deployers to override configuration in
    production
* Adds Boxfile for testing on pagodabox
* htaccess file lets you change rewrite base with an env variable
* Update minion script for moved index.php
Add Vagantfile and Boxfile for easier testing