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As per https://forum.sympl.host/t/auto-updating-ssl-certs-with-custom-apache-site-config/69/3

One of the ways around this under symbiosis was to add an IncludeOptional directive to the master templates (ssl.template.erb & non_ssl.template.erb) with customisations kept in, say, config…

IncludeOptional /srv/<% domain %>/config/apache-*.conf

Thanks to alphacabbage1 for the suggestion.

This will need checking for security, as we don't want any random user writing stuff to there, and breaking the security model or stopping Apache from starting.