Update default config files based on code review in twilio/OpenVBX#261

- Merged `autoload.php` from EllisLab/CodeIgniter@88cf55bd294e74c71e70406e3a48e722db224f7f
- Reenabled `$config['enable_query_strings']`
Remove superceded code

- Removed commented code per code review in twilio/OpenVBX#261