For what its worth, this is the script I use:
#! /bin/sh
#
# Wrapper script for the Microsoft Visual C++ compiler (cl) to allow it to
work with Cygwin based makefiles.
cmd="/c/Program\ Files/Microsoft\ Visual\ Studio/VC98/Bin/cl"
for option
do
case $option in
-I/*)
path=`expr $option : '-I/\(.*\\)'`
cmd="$cmd -IC:/cygwin/$path"
;;
/*)
path=`expr $option : '/\(.*\\)'`
cmd="$cmd C:/cygwin/$path"
;;
*)
cmd="$cmd $option"
;;
esac
done
echo $cmd
eval $cmd
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