need to cygpath the jar file or jar will fail under windows/cygwin.

$ hg qdiff
diff --git a/tools/scripts/compareBuilds b/tools/scripts/compareBuilds
--- a/tools/scripts/compareBuilds
+++ b/tools/scripts/compareBuilds
@@ -36,6 +36,30 @@
   exit 0
 fi

+CYGPATH=''
+platform=''
+case "`uname`" in
+ Darwin*)
+ platform='mac'
+ ;;
+ CYGWIN*)
+ platform='cygwin'
+ CYGPATH="cygpath -m"
+ ;;
+ Linux*)
+ platform='linux'
+ ;;
+esac
+
+doCygpath() {
+ if [ "${CYGPATH}" ]
+ then
+ eval ${CYGPATH} "${1}"
+ else
+ echo "${1}"
+ fi
+}
+
 echo "Comparing rt/build files:"
 (cd "$one";
  find build -type f | sort > /tmp/build-files-one
@@ -66,8 +90,8 @@
         jar=${i##*/}
         jar=${jar%.jar}
         echo "Comparing JAR $i $jar"
- jar tf ${one}/$i | sort > /tmp/files-one-$jar
- jar tf ${two}/$i | sort > /tmp/files-two-$jar
+ jar tf `doCygpath "${one}/$i"` | sort > /tmp/files-one-$jar
+ jar tf `doCygpath "${two}/$i"` | sort > /tmp/files-two-$jar
         comm -13 /tmp/files-one-$jar /tmp/files-two-$jar | while read f
         do
             echo " new: ${f}"