Add autogen.sh

We want ./configure to be an auto-generated file.  Now, instead of
running `./configure`, you run `./autogen.sh && ./configure`.
Add a `make TIMED=1` option

Copied from coq_makefile.

Also, make some paths hopefully a bit more robust to building in a
different directory.
Add an `html` target

Mostly copied from coq_makefile.  I'm not sure if I got the links into
the standard library correct.
Merge branch 'make-html' of https://github.com/JasonGross/HoTT into JasonGross-make-html

Conflicts:
	Makefile.am
	Makefile.in
	configure

I put back in the files generated by autoconf to make ordinary people's
lives easier. I hope Jason can live with "the churn".