This simple rewrite will help you to run phpunit from PHPStorm in Vagrant box without patching php.jar

vhost.conf

    location ~ ^/_intellij_phpunit_launcher.php$ {
        expires        off; ## Do not cache dynamic content
        set            $args  "$args&dir=$document_root&config=phpunit.xml.dist";
        fastcgi_pass   unix://var/run/php5-fpm.sock; # Replace with your fpm pass
        fastcgi_read_timeout 600;
        include        fastcgi_params; ## See /etc/nginx/fastcgi_params
    }

thanks for this!