The rewrite router can be used in subdirectories (e.g.,
http://domain.com/user/application-root/) in which
case the base URL of the application
(/user/application-root) should be automatically
detected by Zend_Controller_Request_Http and used
accordingly.
Should the base URL be detected incorrectly you can override it with
your own base path by using
Zend_Controller_Request_Http and calling the
setBaseUrl() method (see Base URL and Subdirectories):
<?php
$request->setBaseUrl('/~user/application-root/');