What _should_ the permissions be on these files? The upgrade failed because some directories didn't have write permission for the process user, but once that's fixed I now get this instead ...

They should be readable by the system. This would generally however indicate you dont have the latest files so I would check that before anything else

I downloaded the full suite again as suggested.

I've run into this issue now every upgrade since we purchased & installed the Commerce add-on, that was a manual install and it's left files with wonky permissions all over the place, so the automatic upgrade doesn't work any more 😞

Note, the software will use the standard permissions used by your web server. If you need alternative permissions for specific types of files, I can provide you the constants entries to do that, but you would need to know what those permissions need to be from your hosting company. The issue at present is the software cannot read those files

I run into issues when I copy files in to place because I run IPS inside docker so the user IDs don't match up & the host user doesn't have the right permissions inside Docker. I try and update them but I always miss a couple. Once I've got them all the automated update will work again and I can stop looking for needles in haystacks.

Excellent. Glad you were able to find the issue. I would advise keeping a checklist to help you in cases like this if you need to upload files. If you run into this often, simplifying your setup may be the best route 🙂 .

It used to work perfectly, but then I had to install the commerce extension manually and it stuffed up a bunch of permissions. It feels like every update I get closer to being able to just do it automatically once again 🙂