.gitignore: ignore generated source docs, don't ignore Doxyfile.help

Doxyfile.help isn't generated
git_prompt: Fix bad test if bash.showUntrackedFiles isn't set
git_prompt: Default upstream_prefix to nothing

git.git's __git_ps1 doesn't have an upstream prefix. I'm not sure why
one was added to our __fish_git_prompt, but it certainly shouldn't
default to a space.