After the update, I noticed that several images (including /resources/assets/logo.png) are missing. I think it's possible (for the logo at least) that they were deleted during the update. I don't know why that would have happened, and I can't seem to find any trace of them anywhere.
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I fixed it. Avatars key need to be reuploaded though. I had to reclone the git repo because of conflicts. When I moved the images folder back to the document root, I forgot to delete the already existent images folder resulting in the images being in /var/www/html/images/images
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Any idea what happened to the usual logo though? It was originally located at /var/www/html/resources/assets/logo.png
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I had to re-fork the repo as well. I forgot that I had put it there. Anyway current one will work fine. Probobly better to use an on-wiki version anyway.