Question
Where should I add customizations to Apache?
Answer
Customizations made directly to Apache's configuration file are overwritten when the Apache configuration is rebuilt. Instead you will need to use Apache includes to prevent your changes from being overwritten. Custom changes should be made via the WHM / Service Configuration / Apache Configuration / Include Editor interface.
When Apache's configuration is rebuilt, and the service restarted, the changes made to your includes will be included with Apache without the need to write them directly into the configuration file.
Additional Resources
How to use Apache includes to add configuration directives to a specific domain's VirtualHost
How to use Apache includes to add configuration directives to all VirtualHosts sever-wide
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