Message3352

The source of the problem seems to be the following lines of build.xml:

    <target name="jar-complete" depends="compile,expose,jarjar">
       <jar destfile="${dist.dir}/jython-complete.jar">
          <fileset dir="${compile.dir}"/>   
          <fileset dir="${exposed.dir}"/>
          <fileset dir="${jarjar.dir}">

This would explain the two PyArray.class files: One for the non-exposed
version from ${compile.dir} and another from ${exposed}.dir

I'm attaching a patch to put first the exposed class into the jar and
use the duplicate="preserve" attribute on the task, to completely avoid
duplicates.