What does "roll your eyes" mean?

You (quite literally) roll your eyes when you don't believe something or don't care about it. In this particular case, it is implied that you might be so familiar with the protocol that it's all old news to you. It's all over the place, nothing special, so seeing it yet again makes you roll your eyes.

Roll eyes means turn (one's eyes) upward, typically to show surprise or disapproval.

Sarah rolled her eyes.

I've never seen this phrase used in the context of technical documentation. The phrase is often used specifically in the context of teenagers rolling their eyes at something their parents, or another authority figure, is saying. Given this context I believe the sense of "rolling your eyes" includes a connotation of silent resistance, or only grudging acceptance, of that authority figure's pronouncement. The resistance could be to excessive repetition, or it could be resistance more generally to the right of the speaker to make the statement or issue the instruction that is met with rolling eyes.

Yes, you do "roll your eyes" upward to express disbelief.

To the heavens, specifically, as in "Saints preserve us, is this guy for real?!"