app.yaml in different directory than main.js?

I have a Node.JS application that I want to deploy on AppEngine. At the moment I am getting following error:

Beginning deployment of service [default]...
Building and pushing image for service [default]
ERROR: node.js checker: Neither "start" in the "scripts" section of "package.json" nor the "server.js" file were found.
ERROR: (gcloud.app.deploy) Your application does not satisfy all of the requirements for a runtime of type [nodejs].  Please correct the errors and try again.

This makes sense as this is the folder structure:

• client
• server
  • main.js
• app.yaml

As you can see I have a separate folder for my client code and server code. If I put the app.yaml file inside the server folder, the deployment works but when I try to access the app it cannot find the client files as they were not part of the deployment.

Is there anyway to configure this in the app.yaml or do I need to refactor my app?

via Passero