I got this work now, We have reinstalled our server and now everything is working but the terminal link back on breadcrumbs issue, which reported as bug. Here is my code tested at
http://aro.koyauniversity.org/
In Config file
base_url[index] = http://aro.koyauniversity.org
base_url[aro] = http://aro.koyauniversity.org
restful_urls = on
and in the htaccess, please note that I needed that redirection as base domain do not work and show error, of page not found.
RewriteEngine On
RewriteCond %{HTTP_HOST} ^aro.koyauniversity.org$
RewriteRule ^$ http://aro.koyauniversity.org/index [L,R=301]
RewriteEngine on RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-d RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteCond %{REQUEST_FILENAME} !-f RewriteRule ^/index/(.*)$ /index.php/index/$1 [L]
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-d
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/aro/$1 [L]