From the command line you could try:

./openerp-server -u all -d <db_name>

This will update all modules including your base modules. But be careful though, I have faced several issues when updating all modules. Sometimes, some random menus start appearing and on more than one occasion, my database has become completely unusable. Usually, running the same command again seems to fix the issue, but I'm not sure what causes it. If you want to change something in the XML, it would be best to do it in a custom module or to edit the XML from the front-end.

EDIT:

If you are running it as a service, first stop the service. Assuming that the service is called odoo-server,

sudo service odoo-server stop

Then change the current user to odoo:

sudo su - odoo -s /bin/bash

Then make sure that you are in the odoo installation directory i.e. there should be a file called openerp-server in the directory. Then run openerp-server.

./openerp-server -u all -d <db_name>