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My Let's Encrypt auto-renew actions stopped working recently, and I've narrowed it down to this line in the .htaccess file in the root level of each domain:
# security rules:
# - deny access to files not containing a dot or starting with a dot
# in all locations except installer directory
RewriteRule ^(?!installer)(\.?[^\.]+)$ - [F]
I'm not enough of an Apache guru to figure out how to change this rule to allow access to files in the .well-known directory as well as the installer directory.
I'm running Webmin 1.870 and Virtualmin 6.02 on CentOS 7.1