CodeIgniter multiple application with subdomains and correct htaccess

first thing i would do is move the 'system' folder outside your 'public_html' folder and change your pathing in the various index.php files to reflect the new path. This makes the 'system' folder inaccessible via the web. But still accessible to the application folders.

as for the htaccess file in the subdomain folders i am not all the well versed in the htaccess commands but a quick google search turned up this :

RewriteCond %{HTTP_HOST} !^www\.
RewriteCond %{HTTP_HOST} ^([^\.]+)\.domain\.com$ [NC]
RewriteRule ^(.*)$ http://domain\.com/subdomain/index.php/$1 [L]

just replace : 'subdomain' in the last line with the appropriate folder name.

hopefully this helps

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