Certbot automatically deletes the acme-challenge directory if it is empty; Certbot does not delete the .well-known directory.
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Good to hear that you got it working! May I ask if you have moved the /var/lib/letsencrypt directory over from another box, or modified the permissions in any way manually (or know about running a script / backup recovery process etc. that might have done so)? I'm trying to figure out if this is a bug in Certbot directory creation code.
The Apache plugin doesn't create any files under the active webroot (existent or not). Instead it adds configuration directives in to your VirtualHost configuration. The meaningful to explain the behavior being:
RewriteRule directive to point all requests coming towards /.well-known/acme-challenge/* to be served from /var/lib/letsencrypt/http_challenges
These are also automatically removed by Certbot after the validation.
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