You may find a few tutorials on the web, specifically covering PhpStorm in the app engine development environment, such as this one. If you prefer using Eclipse, it may prove worthwhile reading the "Deploying App Engine Standard Applications from Eclipse" documentation page. The Cloud SDK offers you a dev_appserver to run your app locally prior to deploying. In case using Eclipse is not a must, you can simply follow the tutorials and quick starts linked to from the "PHP on Google App Engine" page.
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Well, I think I almost got the app.yaml right. I am trying to shoehorn an existing app onto gc. Now when I try starting it I get "direct access not allowed.", which sounds like it is directly trying to start a index.php file in codeigniter. I am actually on vacation this week in Norway, so I will wait until I get back to my to work on it.
My next step after getting the app to start will be configuring the mysql.
One more thing, I found a primer on using phpstorm with gc. There was also a video on using the phpstorm gc plug-in. I later found a doc that said that support in phpstorm for gc plug-in was discontinued. Very disappointing.
It may be worthwhile mentioning that you cannot perform local disc access in app engine, so you need to shoehorn the app accordingly.