The JDK jarsigner always puts the manifest at the beginning of a JAR file; but
the Netscape's signtool puts the manifest at the end of a JAR file.

The current JarInputStream implementation cannot verify a jar file signed
by Netscape' signtool since it doesn't even read the manifest in such a JAR
file.

JarFile can verify JAR files signed by Netscape's sihntool; but JarFile only
works with files, not other kind of inputstreams.

When you pass a JAR file signed by Netscape's signtool (e.g.,
/home/shliu/public_html/testJAR/getpropThawe.jar) to the
TestJarInputStream, you get exceptions; but the TestJarFile does get
the manifest from that JAR file.
 
=========================== TestJarInputStream.java ================
import java.util.jar.*;
import java.net.*;
import java.io.*;

public class TestJarInputStream {

    public static void main(String[] args) throws Exception {

        isJarSigned(new URL(args[0]));
        System.out.println("Okey:" + args[0]);
    }

    /*
     * Verify a jar file is signed by a signer with a certificate which can be 
     * traced back to a trusted CA.
     */
    private static void isJarSigned(URL jarURL)
        throws IOException
    {
        String jarURLString = jarURL.toString();

        URLConnection connection = jarURL.openConnection();
        JarInputStream jis = new JarInputStream(connection.getInputStream());

        Manifest man = jis.getManifest();
        if (man == null)
            throw new JarException(jarURL.toString() + " is not signed.");

    }    
}

============================= TestJarFile.java ===================
import java.util.jar.*;
import java.net.*;
import java.io.*;

public class TestJarFile {

    public static void main(String[] args) throws Exception {

        isJarSigned(args[0]);
        System.out.println("Okey:" + args[0]);
    }

    /*
     * Verify a jar file is signed by a signer with a certificate which can be 
     * traced back to a trusted CA.
     */
    private static void isJarSigned(String fName)
        throws IOException
    {
        JarFile jf = new JarFile(new File(fName));

        Manifest man = jf.getManifest();
        if (man == null)
            throw new JarException(fName + " is not signed.");

    }    
}