Because of a bad experience with PHPBB and how hard it was to upgrade the software with updates installed, I've been wary about making many changes to the built-in XF product.
We have a fully developed main site, plus XF. Since we want them to look like one offering, we inevitably have to make some changes. So far, we've been handling them this way:
- CSS - we override XF styles in our self-contained CSS files that are included site-wide
- HTML - we use the template modification system to find/replace blocks of text, as minimal changes as possible as I know this is a danger zone for forum upgrades
- JS - ??
This is specifically for updating things like Redactor, which contains buttons we don't want to be displayed, but also things like moving the Spoiler button outside of the dropdown where no one ever finds it. There are some other things we need to update as well.
If the only option is to physically change the core JS files and deal with merge conflicts later, so be it. Just wasn't sure if there's a better/less risky option.