I’ve worked with helping beginner students set up their environments a bit. I’m skeptical of the idea of providing too much in the way of custom dotfiles or anything like that. Students will come with their own systems. Mac, or Windows, usually. So a professor or grad student who naturally uses Linux and isn’t really a software deployment expert might have trouble getting a rock-solid portable collection of scripts. It might seem like an odd difficulty for smart and technical people to have, but administrating other people’s systems is a totally different skill from research after all!

More importantly, in a class of a couple hundred, somebody will find a way to get off the happy path. No matter how well you design it. Hopefully they’ll come to a teaching assistant or something, but there’s a good chance they’ll go to YouTube or something instead. In that case, it is best if their installation is as standard as possible.

Also the filesystem problem is such a thing and you have dredged up some feelings, hahaha. In particular, I think operating systems and VSCode have gotten way too good at hiding the fact that the file somebody is editing is, in fact, still in a zip archive. Until they go to save it or run it.