Replace `\autoref` with `\cref` throughout.

I propose that we need two pairs of eyes on this pull request because it touches all LaTeX files.

This pull request removes `\autoref` throughout and replaces it with `\cref`. Before agreeing to it I would ask that you actually test it because it is big & fat. It works for me. Also, it might break the hlatex stuff, @JasonGross should be able to tell.