I have Codeigniter installed and working for my main site.

But I am now trying to add an add-on domain to the same hosting account, so I can have two sites running on the same hosting. Add-on domains make a new folder in the main public_html folder to store the web files.

How can I get Codeigniter to ignore this directory? The site doesn't load properly when I try and view it.

I have an SSL on the main site too and redirection for www URLS. Here's my .htaccess file:

RewriteEngine on
Options +FollowSymLinks
RewriteBase /

RewriteCond %{HTTP_HOST} ^www\.mysite\.co.uk$ [NC]
RewriteRule ^(.*)$ http://mysite.co.uk/$1 [L,R=301]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /index.php/$1

RewriteCond %{HTTPS} off
RewriteCond %{REQUEST_URI} (site|sections|here)
RewriteRule ^(.*)$ https://%{SERVER_NAME}%{REQUEST_URI} [R=301,L]

RewriteCond %{HTTPS} onsite|sections|here)
RewriteRule ^(.*)$ http://%{SERVER_NAME}%{REQUEST_URI} [R=301,L]