In PHP development environments, it is not entirely uncommon to use an auto_prepend_file to add development-specific functionality to an application.
Usually such a file is used for several projects at the same time. This means the prepend file resides somewhere in a more high-level location.
A more common practice is to use Xdebug te debug PHP code.
When combining these two with PhpStorm this will lead to the prepend file being marked as "not mapped".