Generate the symlinks in configure again

I don't see any other way to permit the use of either the bundled coq,
or a system one; we might not have the version of OCaml used to compile
the system Coq.

This closes #201.
Test with bundled and global Coq on travis
Improve symlink code
Make the Makefile actually work with bundled coq

Before, it was looking for it to be already installed.
Change to the right directory for travis
Try harder to install coq on travis
Be a bit noiser about changing directories
Get rid of the pwd

Things seem to be working now
travis: coq is in /usr/local/bin, not /usr/local
travis: Fix the path to coq
Add --without-bundled-coq to autogen, fix make

You can now call './autogen.sh --without-bundled-coq' to not init the
submodule.

Passing COQBIN to ./configure now disables the execution of ./configure
in coq-HoTT.

When not using the bundled Coq, we no longer make the miniopt target in
coq-HoTT.  I was originally doing this to build just the required
plugins, so we can statically link to them.  But I gave up on this
eventually (at least for now), and so we no longer make the miniopt
target.
Add some coq cleaning targets
Make autogen message a bit nicer
Update INSTALL
Remove 'secret' from INSTALL
Better support for --disable-bundled-coq