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This isn't really true. You just need to configure a redirect from the naked domain to your serving URL, at www.

For example, my site (justbeamit.com), runs on GAE, but the naked domain simply redirects to the www.

I thought about adding an edit in there to clarify you could do that, but I think the points remain that in the end, you still end up with www. in the URL bar.

The real reason is because you cannot add a CNAME record using the zone apex.

AWS gets away with this afaik with some magic to point to the IP address for the loadbalancer that would serve your content.

Techincally you can find the IP address for your GAE subdomain and add an A record for your apex domain, but keep in mind that this is a bad idea.

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