Algo parecido com isto:
# These go in the VirtualHost context.
RewriteEngine On
RewriteCond %{HTTP_HOST} ^www\.(.*)$ [NC]
RewriteRule ^(.*)$ http://%1$1 [R=301,L]
RewriteCond %{REQUEST_URI} ^(/welcome(/index)?|/index(.php)?)/?$ [NC]
RewriteRule ^ / [R=301,L]
RewriteRule ^/(.*)/index/?$ /$1 [R=301,L,NC]
RewriteCond %{REQUEST_URI} ^/system [NC]
RewriteRule ^/(.*)$ /index.php?/$1 [L]
<Directory /path/to/docroot>
# This is so that these have the correct filesystem path in the
# REQUEST_FILENAME parameter.
# If you already have a <Directory> for here, add these to it.
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)/$ $1 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l
RewriteRule ^/(.*)$ /index.php?/$1 [L]
</Directory>