configure: fix paths on cygwin
configure: fix paths on cygwin

Long story short: Filname.concat and other OCaml provided functions
to be "cross platform" don't work for us for two reasons:
1. their behavior is fixed when one compiles ocaml, not when one runs it
2. the build system of Coq is unix only

What is wrong with 1 is that if one compiles ocaml for windows
without requiring cygwin.dll (a good thing, since you don't need to
have cygwin to run ocaml) then the runtime always uses \
as dir_sep, no matter if you are running ocaml from a cygwin shell.
If you use \ as a dir separaton in cygwin command lines, without
going trough the cygpath "mangler", then things go wrong.

The second point is that the makefiles we have need a unix like
environment (e.g. we call sed).  So you can't compile Coq without
cygwin, unless you use a different build system, that is not what
we support (1 build system is enough work already, IMO).

To sum up: Running coq/ocaml requires no cygwin, comipling coq requires
a unix like shell, hence paths shall be unix like in configure/build stuff.

mattam82/coq,Zimmi48/coq,amintimany/coq,william-lawvere/coq,maximedenes/coq,Zimmi48/coq,william-lawvere/coq,TOSPIO/coq,Matafou/coq,gmalecha/coq,silene/coq,ppedrot/coq,ppedrot/coq,Zimmi48/coq,herbelin/github-coq,ejgallego/coq,william-lawvere/coq,jpdeplaix/coq,mlasson/coq,maximedenes/coq,coq/coq,Lionel-Rieg/coq,letouzey/coq-wip,Matafou/coq,maximedenes/coq,SkySkimmer/coq,mlasson/coq,asr/coq,ejgallego/coq,gares/coq,maximedenes/coq,SkySkimmer/coq,Ptival/coq,gares/coq,TOSPIO/coq,TOSPIO/coq,barras/coq,gares/coq,herbelin/github-coq,TheTypoMaster/coq,Lionel-Rieg/coq,ale-f/coq,silene/coq,Lionel-Rieg/coq,letouzey/coq-wip,ppedrot/coq,silene/coq,TheTypoMaster/coq,letouzey/coq-wip,gares/coq,gares/coq,Zimmi48/coq,8l/coq,JasonGross/coq,JasonGross/coq,mattam82/coq,letouzey/coq-wip,8l/coq,jpdeplaix/coq,SkySkimmer/coq,mlasson/coq,ejgallego/coq,TheTypoMaster/coq,JasonGross/coq,Ptival/coq,Ptival/coq,ale-f/coq,Matafou/coq,barras/coq,herbelin/github-coq,coq/coq,barras/coq,ale-f/coq,amintimany/coq,JasonGross/coq,gmalecha/coq,8l/coq,letouzey/coq-wip,asr/coq,coq/coq,ejgallego/coq,mattam82/coq,coq/coq,gmalecha/coq,maximedenes/coq,asr/coq,SkySkimmer/coq,jpdeplaix/coq,ppedrot/coq,ppedrot/coq,amintimany/coq