site hacked - all javascript gone

[eluser]vincej[/eluser]
All the js source files are still there ie jquery, colobox etc. What I mean all the js is gone off the pages. I know it is a hak as they left some delightful messages behind. Can some one tell me what kind of hack this is indicative of and how I might better protect my site ?

Thanks !

[eluser]Otemu[/eluser]
A number of ways this could of happen, but you don't provide much information on your site, cms? hosting company? framework? environment? etc

With limited information I can only point you in the direction of a guide http://www.creativebloq.com/web-design/w...te-7122853

[eluser]vincej[/eluser]
Thanks ! I was wrong - they did not get all the js. I am using CI 2.1.4. and built a custom business app. I have upgrade to 2.2. I think thy got in either with SQL injection, so your links to testing tools is helpful. It's hosted at InMotionHosting on a VPS. When they got in there used the control panel to delete all the pages. I have learned from Google that CI's xss_clean tool is useless from a protection point of view. Correct ??