I agree. I kept trying to "ls" and observe what was going on between each command or examine the directory structure of /.git and so on. Only later did I realize that there was a filesystem explorer-like window below.

Also, having them automatically adding files to the directory was kind of confusing. Sometimes I would type a command and something new would appear in the file system as a result of that command. Other times, I would type a command and something new would appear in the filesystem that I suppose was expected to be used for a subsequent step. It would have been nice if these things would have happened in isolation from each other. That way I could run the command, see what happened, and then perhaps click "next" to move onto a different scenario with a new set of files I could add to the repository.