index.php in the public directory is the only way
into the application, you should rewrite all requests to it (you can
use .htaccess in Apache + mod_php, or the
equivalent in your web server, see below).
<?php
define("APPLICATION_PATH", dirname(dirname(__FILE__)));
$app = new Yaf_Application(APPLICATION_PATH . "/conf/application.ini");
$app->bootstrap() //call bootstrap methods defined in Bootstrap.php
->run();
?>