On the Google Cloud Platform blog there's a recent post showing you how to directly integrate the Google App Engine PHP support with the popular PHP IDE PhpStorm for seamless development.
Our IDE for PHP, PhpStorm, provides seamless integration with Google App Engine for PHP - allowing you to locally develop, debug and deploy your PHP applications on Google App Engine. When testing your application locally, we also support full emulation of App Engine services through the App Engine Development server. The [introductory] video shows how to get started with Google App Engine for PHP in PhpStorm. We also have a comprehensive tutorial which covers Google App Engine with PhpStorm in detail.
His example shows how to integrate the IDE with the Google Cloud SQL service. He shows how to create a new user (via the API console) and how to connect that user in PhpStorm. He includes a CREATE statement for a sample table and the PHP code to connect.