Various fixes for cygwin/MSWin

Quote more things so that it works even if COQBIN has spaces.

coq doesn't like cygwin symlinks, so fall back on physical copies

make doesn't like backslashes, so pipe coqdep through sed to fix that
(bug reported at https://coq.inria.fr/bugs/show_bug.cgi?id=3157,
and also to make)

hoq* still doesn't work, but that's for the next commit.  I'm going to try recompiling ocaml, to see if that fixes the `Warning: Cannot open /cygdrive/d/Documents/GitHub/HoTT/coq\theories/*` warnings from getting cygwin-style paths from `readlink -f`.