I agree with you in general, but I feel like you take a wrong perspective of it.
The author takes a top-down approach to teaching, which basically means that he thought about this tutorial from his perspective, someone that was already intimately familiar with the details. This, as you pointed out, is wrong. If this is a tutorial for beginners, you need to have some explanation of what "checking-out" means, what "trees" are, etc. If this tutorial is for advanced users, however, its too sparse to give any new information. So in the end, the tutorial is pretty, but helps neither advanced users nor beginners.
I feel like the examples you give, however, are inefficient for a guide as well -- at what point do we start making assumptions about the reader? For example, you give the example that a beginner might not understand trees, but how do we know they understand anything? Do we believe they don't know trees, but do know how to program, and if so, to what level? Do we assume they are proficient in the terminal, and can even install git if it is not already present? The problem with your approach is that it seems like there's never a point at which we stop.
When I learned a new romantic language (Spanish), we didn't start all the way at the beginning with the alphabet, nor did we try to explain conjugation, past participles. We started with simple phrases -- "Hello", "How are you", "The weather outside is nice", without a real understanding of why we said them. Then, over the years, we peel back the onions of why phrases were the way they were -- Adios (goodbye) was a combined form "A dios"--to the gods. But you shouldn't try to teach that from the onset as you'll overwhelm the learner -- you just continually add on layers until they discover themselves.
Similarly, I feel like for this scenario, a tutorial should set up a scenario that fits the commands perfectly -- don't explain why we use git commit -m, have the first user just go through a few scenarios where they just do it. Then, as they learn, build advanced git tutorials that add on layers, so suddenly they start to uncover all the nuances that git has to offer.
Now, granted, that doesn't extend itself to a "simple guide" if you will, but I feel that these iterative examples that let you think are much better.