Using minimal docroot with no writable dirs

* Move index and .htaccess to httpdocs folder - always use this as docroot
* htaccess file lets you change rewrite base with an env variable
* Update minion script for moved index.php
Incorporate ideas from kohana-projecttemplate

* 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
Move docs on kohana init options to config/init.php
Cleaner environment switching

* default to 'development' invalid environment name used
Add extra detail to the README
Fixing travis build