Roll back doxygen formatting.

This undoes the fancy searching we had, as well as the fancy formatting.

Fixed Doxygen warnings about a stale Doxyfile. I'm using Doxygen 1.8.4; if we
merge this then everyone should use at least Doxygen 1.8.4 and we should note
this Doxygen version in the README.md.

I also fixed some doxygen for AbstractOutput.

This also does something controversial: it removes the sidebar! Are people okay with this? I know @sherm1 said he had some users who demanded the sidebar. For me, it just makes it harder to search for what I want. I'm happy to undo this change though.