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[EP-tech] CGI pages branding missing?

CAUTION: This e-mail originated outside the University of Southampton.
Hi All,

I have recently successfully done my first ever server and EPrints upgrade. Rebuilding the EPrints set-up is going as well as I could hope, but I'm struggling with getting custom CSS/html/JS etc to display on any page that has "cgi" in the url.

E.g. the admin and search pages. Here it remains as the default. On other pages such as homage, EPrints abstracts, views, static it displays with our university branding and custom page layouts, css and so on.

Can anybody tell me what I'm missing? I've been at it all day and can't work out what's happening. I'm confident that all files have been migrated.

Running the "epadmin test" script tells me everything is okay. Any advice would be so helpful.

Thanks,
James