Updated Passenger Documentation for Passenger 4.0.x

Several settings in the example vhost are no longer correct and can confuse users looking to set up Apache + Passenger for their Puppetmasters.  The commented version of Passenger has been updated to 4.0.x to reflect the current state of affairs, the RackAutodetect and PassengerUseGlobalQueue which throw errors and warnings have been removed, the PassengerAppRoot variable has been specified to allow the application to launch, and HTTPD 2.2.x and 2.4.x compatible directives have been added to the Directory permissions for future-proofing.