Update the install script to retry after cleaning

Sometimes, Coq's Makefile is terrible at noticing that things have
changed.  So we try to clean up if `make` fails.

Also, we don't need to patch `configure` anymore; Coq trunk uses a
configure.ml file.
Merge pull request #463 from JasonGross/autoclean-on-make-failure

Seem to work on my Mac.
./autogen.sh