Hi Yaakov,
the attached patch solves some case I hit where the
debuginfo are not properly extracted.
"." as workdir can be managed differently by the build
system and cygport debuginfo extraction when:

$ pwd
/pub/devel/openblas

 $ readlink -f $(pwd)
/cygdrive/e/cyg_pub/devel/openblas


Usually Automake/Libtool are not affected, but Makefile only
build system, like openblas one, are instead,

Regards
Marco
--- /usr/bin/cygport~   2015-07-20 09:12:08.000000000 +0200
+++ /usr/bin/cygport    2015-11-21 17:45:13.583854800 +0100
@@ -395,7 +395,7 @@
 then
        if [ -f ./${cygportfile} ]
        then
-               _topdir=.;
+               _topdir=$(readlink -f .);
        else
                _topdir=/usr/src;
        fi
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