Regarding the table of contents, it took a while to realize the text was clickable. Also I would prefer the arrows to show what they go to. For example "up next: Checking Status"
I don't know whether that would break the design, but it makes it more usable in a motivating sort of way, "oh boy committing is next!"
All in all, I agree with the learn by doing, so very nice job and thanks for all the good work!
Also some sort of hint that the ToC is clickable, I didn't realize that at first either.
Also, it strikes me that the entire guide should be put on GitHub - did I miss somewhere where it says it is?
All in all this is a great resource along the lines of http://hginit.com/ - which is useful, because the mostly brain-dead students at my university tend to take FOREVER to learn DVCSs. I can't tell you how many times I've had to explain that you really only need to 'git clone' once unless you are checking to make sure you got everything 'right' with the push.
Now instead I'll just point people at this.