Extract folders in gradle and create a jar

I have this structure in a zip file

 |--com: A.class, B.class
       |--org: C.class, D.class
 |--android: X.class
 |--stuff: Stuff.inf, info.txt

I want be able to extract only the folders with .class files: com, org, android. And put them on a jar. So far I have dont this:

task createJar {
    //unzip the file
    FileTree zip = zipTree('runtime.jar')
     FileTree zip2 = zip.matching {
        include 'classes/**/*.class'
    zip2.each { file -> println "doing something with $file" }
            //create the jar
                from zip2

But I get the jar with the classes folder on it, like: classes/org/apache/http/entity/mime/content/StringBody.class And i want it like: org/apache/http/entity/mime/content/StringBody.class

Any idea how? Thanks!