My university frowned on any industry-related classes (i.e. teaching software engineering tools vs. theoretical CS), but I was fortunate enough to know a passionate grad student who created a 1-credit seminar course on this exact topic.
This course covered CLIs/git/Unix/shell/IDEs/vim/emacs/regex/etc. and, although I had experience with Linux/git already, was invaluable to my early education (and adoption of Vim!).
It makes sense that this isn't a core topic, as a CS education should be as pure as possible, but when you're learning/building, you're forced to live within an operating system and architecture that are built on decades of trade-offs and technical debt.
I don't think that's a good goal. Otherwise, why let you near a computer at all, and not restrict you to chalk and blackboards?
The syscall ABI itself is remarkably stable, backward compact is practically Linux's religion, but the conceptual model has shifted substantially.
Namespaces and cgroups went from obscure subsystems to the foundational abstraction containers run on.
io_uring rewrote the async I/O model.
eBPF changed how you think about observability and policy enforcement.
Introductory LFD103 is a free course:
https://training.linuxfoundation.org/training/a-beginners-gu...
Some channels to get some experience handling the modern kernel source:
Seriously though, this book is fantastic, and far better than typical course textbooks. I'm honestly a little surprised that universities would select it.