I want to remove the "Comment Internally" from Service Desk. I would like to set up regular commenting within JSD as I would in any other non-SD project. I'm not sending my users to the Customer Portal as I don't have an interest in using it at this point. Is there a way that I can disable "Comment Internally" or rename the comment button so that only regular commenting is available?
There isn't a built-in way to do this, but it can be implemented externally. You want to be able to change the CSS on the issue pages accepting comments. In order to achieve this, you'll have to implement a reverse proxy to act as the webserver front-end. On this proxy you will need to filter for the element containing the button and alter it (hide visibility, etc.). It's not an easy hack, start by looking at this page and then test your own methods:
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