Modified configurations

1. renamed 'example.htaccess' to '.htaccess'
2. removed 'index.php' from the URL by changing the RewriteBase in
.htacess
3. moved and renamed /system to /kohana/3.3.1 for easy update
4. changed $system in in index.php
5. enabled 'database' and 'orm' modules in bootstrap.php
6. implemented hello world properly (with Controller_Welcom & site.php)