The AtomArray.php is the data file that the web pages pull the information from and should be set to go into the root.
All of the web pages that are in the root use include("AtomArray.php"). Since the main AtomFeed files are in another folder, you need to use this setting:
$file_output = "../AtomArray.php";.
If you omit off the ’ …/ ', it will keep the AtomArray.php file in the sub folder and the include function for the web pages will not get the file and create an error.