It's fairly common for an institution to have web branding standards that need to be applied to all pages of the site, and that might include all pages of an OJS site. We can, of course, customize some aspects of the site using the sitestyle.css and journalStyleSheet.css files, but what about customizations that require changes to the HTML code? What's the best way to manage such changes?
In particular, are there some changes that are so commonly desired that they are worth catering to specially? For example, providing framing such as a header that would always appear above the PKP-provided header? Since individual journals allow specification of a custom html footer, a global site-specific footer is perhaps less needed that a global site-specific header.
What I've been doing is modifying the templates in lib/pkp/templates/common, e.g. modifying header.tpl to add mandated branding. However, I don't like the idea of having local changes to core application code mixed in like that -- too easy to have it break when a new version comes out. Would it be worthwhile to add a hook in that file (perhaps just before or after <div id="container">) to include a corresponding file from public/site if such existed?