The content of this dispute is explained in http://www.apache.org/jcp/sunopenletterfaq.html. Apache Harmony is an independent, clean implementation of Java. It has nothing to do with classpath (or Classpath).

The dispute centers around the specification lead's apparent refusal to offer license terms to Apache for the JCK which are open source compatible. Apache is a charity and can (by charter) only ship open source software.

The process under which the specification was developed is meant to gaurantee that open source implementations are possible for every specification. No license has yet been granted for any independent open source implementation.