code: protected void zipFile( InputStream is, ZipArchiveOutputStream zOut, String vPath, long lastModified, File fromArchive,
                              int mode, String symlinkDestination )
          throws IOException, ArchiverException
      {
          if ( MANIFEST_NAME.equalsIgnoreCase( vPath ) )
          {
              if ( !doubleFilePass || skipWriting )
              {
                  filesetManifest( fromArchive, is );
              }
          }
          else if ( INDEX_NAME.equalsIgnoreCase( vPath ) && index )
          {
              getLogger().warn( "Warning: selected " + archiveType + " files include a META-INF/INDEX.LIST which will"
                                    + " be replaced by a newly generated one." );
          }
          else
          {
              if ( index && ( !vPath.contains( "/" ) ) )
              {
                  rootEntries.addElement( vPath );
              }
              super.zipFile( is, zOut, vPath, lastModified, fromArchive, mode, symlinkDestination );
          }
      }
docs: Overridden from Zip class to deal with manifests and index lists.