> my staged files disappear from my list of file changes
> a new commit is appended to my git log
> my branch ends up with a new head commit, diverging from its upstream
> If you create a commit from the command line, you see none of this.
Sure, if you're not using an addon like powerline-shell. If you do, all of those are immediately obvious.
I'd argue it's less "commandline bad" and more "stock commandline bad."