Fix install script for Make >= 4.0

This works around https://github.com/HoTT/coq/issues/69.  For the time
being (until we get a better version of Coq), we simply patch Coq's
configure script.

Also add a note about running scripts on Windows.
Merge pull request #340 from JasonGross/patch-configure

Fix install script for Make >= 4.0