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I have a GAE app and a custom domain registered on enom.com. The app is a static website that's configured by app.yaml.
I'm trying to use LetsEncrypt certs for ssl, so I want to have valid certs for both www.example.com and example.com. I can get the cert for www.example.com working fine.
However the problem is in my naked domain. Whenever a http request goes to http://example.com/, it gets redirected to http://www.example.com/, ok. But, if a http request goes to e.g. http://example.com/a.html, the request is still redirected to http://www.example.com/. So when LE servers come looking for their well-known acme-challenge, it fails because they see index.html.
I guess this isn't a common behavior because no one is mentioning this, not at https://code.google.com/p/googleappengine/issues/detail?id=10802, nor at https://github.com/certbot/certbot/issues/1480.
I've tried to dig into why this is happening, one error I can see is here:
If I select to overwrite, GAE says it "failed to insert mapping"
This whole project was started by another person and he claims he's not aware of example.com being assigned anywhere else. I've looked at his Google Cloud Console and it would seem that he's correct.
Maybe something of interest is that in the Domain page of admin.google.com, naked domain redirect is set up. It redirects example.com to www.example.com. I've not found a way to disable it.
On my dns registrar, I have input the four A records, four AAAA records, and a www for CNAME.
TL;DR: My LetsEncrypt acme-challenge is failing for my naked domain, help!

I started getting the same error in app_engine after I went to Google Apps account and added example.com to redirect to wwww.example.com. After I did this, in app_engine I got "is already mapped" error. And there was no way to undo the redirect in Google Apps, so my guess was that Google Apps had mapped it and so App Engine could not modify it or add it. I had to explain this to Support team, and btw Google Apps support is free to call, so contact them and then get transferred to App Engine support team.
There is no way to fix it yourself, you have to get Google Support on call and explain clearly and they can reset. I was bounced between Google Cloud and Google Suites (Apps) support teams 7 times and after 2 weeks finally resolved, each one blaming the other, until I found a guy who understood this issue and fixed it for me.