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Latest documentation on app.yaml recommends removing application and version element.
https://cloud.google.com/appengine/docs/standard/python/config/appref
At least for my case, gcloud would complain if these elements are present.
For setting up environment variables, I haven't found gcloud equivalent of appcfg.py --env_variable.
Since it is not clear for someone not familiar with app engine that appcfg.py is not available from the new Google Cloud SDK, I would say removing these instructions reduces confusion.