Can't access my code igniter 3 website

My website has been working for almost a year and then it suddenly stopped loading. When I go to the link it just keeps loading. I am hosting on a shared server. I found this error on the cpanel:
 client denied by server configuration: /site.com/system/
[i] client denied by server configuration: /site.com/application[/i]
[i][i] client denied by server configuration: /site.com/php.ini[/i][/i]

I can access HTML pages that I put at the root of the website but not PHP ones. 
By renaming the index.php and changing from the build from production to development and vice versa, the website works for a short period and the problem reoccurs. I'm assuming the problem is the .htaccess file and apache. 
Any ideas on how to solve the problem?