item.url generated at menu issue
I think you may need to enable apache mod_rewrite. You can refer this answer as well. To enable mod_rewrite, use the following command:

a2enmod rewrite


Then you need to restart apache for the changes to reflect,

sudo /etc/init.d/apache2 restart


or

sudo service apache2 restart


Refer this page for information about clean urls, this might even help.