public folder on codeigniter and clean URL
Your .htaccess has some strange spacing issues that break the site when I replicate them on one of my codeigniter sites. I would try with these changes.
<IfModule mod_rewrite.c> Options +FollowSymLinks RewriteEngine On RewriteCond %{REQUEST_FILENAME} !-d RewriteCond %{REQUEST_FILENAME} !-f RewriteRule ^(.*)$ index.php?/$1 [L]</IfModule>