git prompt improvements (indent, staged, comment)

Started these commits because I noticed it wasn't displaying the staged token even with __fish_git_prompt_showdirtystate set.  Turns out the relevant function wasn't actually outputting the token after figuring out what it should be.

Re-indent patches are annoying, but several nested if statements weren't lined up properly and it used two different kinds of indenting.  I couldn't follow it as is, so I fixed it.

Finally, I replaced a short "what is this" style comment with a short explanation and gave a longer one in the commit.