Android Proguard java.io.IOException: Can't read [proguard.ClassPathEntry
ProGuard can't find (or read) one of the input jars. If you install ProGuard 4.5.1 instead of 4.4, it will print out the proper file name, so you can find out why it is missing.
Download the latest ProGuard and replace the it's existing lib folder in your base sdk tools folder (ex. c:/android-sdk/tools/proguard) with the new one you've downloaded.
Like Eric said, it will then tell you what's missing. More than likely you've used the wrong path in -libraryjars command. Try removing
Updating ProGuard did help to track down the problem. In my case it was to do with the JDK configuration on my Mac and the rt.jar and jsse.jar files not being located in the usual place.
I found the solution here.
cd $JAVA_HOME/lib
sudo ln -s ../../Classes/classes.jar rt.jar
sudo ln -s ../../Classes/jsse.jar .