In addition to wat Jason said, you might also want to take at the 
"includes" directive to avoid repeating yourself: 
https://cloud.google.com/appengine/docs/standard/python/config/appref

So you could do something like:

- have a common "services.yaml" somewhere
- in each of the dev / stage / prod yaml just put the information specific 
for that env and include the common services yaml

Sidenote: we have a small helper script for our GAE projects so that we can 
do some more processing around running / deploying and we generate our 
app.yaml's dynamically:

def _buildAppYamls(for_deployment):
    app_yaml_templates = _findInAppengineModules('app-template.yaml')
    for template in app_yaml_templates:
        content = _load(template)
        d = os.path.dirname(template)
        module = os.path.basename(d)
        if module != 'main':
            module_tag = 'service' if for_deployment else 'module'
            content = '%s: %s\n%s' % (module_tag, module, content)
        if not for_production:
            content = 'version: local-development\n' + content
        with open(os.path.join(d, 'app.yaml'), 'w') as f:
            f.write(content)

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