Program: 100666
Project: 100666
Buggy source:
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  Attributes res=atts;
  if (MAP_TOPICREF.matches(res)) {
    final URI href=toURI(res.getValue(ATTRIBUTE_NAME_HREF));
    final String scope=res.getValue(ATTRIBUTE_NAME_SCOPE);
    final String format=res.getValue(ATTRIBUTE_NAME_FORMAT);
    final String processingRole=res.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
    if (href != null && (scope == null || scope.equals(ATTR_SCOPE_VALUE_LOCAL)) && (format == null || format.equals(ATTR_FORMAT_VALUE_DITA)) && (processingRole == null || processingRole.equals(ATTR_PROCESSING_ROLE_VALUE_NORMAL))) {
      final URI file=stripFragment(href);
      Integer count=topicrefCount.containsKey(file) ? topicrefCount.get(file) : 0;
      count++;
      topicrefCount.put(file,count);
      if (count > 1) {
        final String copyTo=res.getValue(ATTRIBUTE_NAME_COPY_TO);
        if (copyTo == null) {
          final URI generatedCopyTo=generateCopyToTarget(href,count);
          final File source=resolve(currentFile.getParentFile(),toFile(file));
          final File target=resolve(currentFile.getParentFile(),toFile(stripFragment(generatedCopyTo)));
          final File relSource=getRelativePath(new File(job.getInputDir(),"String_Node_Str"),source);
          final File relTarget=getRelativePath(new File(job.getInputDir(),"String_Node_Str"),target);
          copyToMap.put(relTarget,relSource);
          final AttributesImpl buf=new AttributesImpl(atts);
          XMLUtils.addOrSetAttribute(buf,ATTRIBUTE_NAME_COPY_TO,generatedCopyTo.toString());
          res=buf;
        }
      }
    }
  }
  getContentHandler().startElement(uri,localName,qName,res);
}

Fixed version (ground truth):
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes atts) throws SAXException {
  Attributes res=atts;
  if (MAP_TOPICREF.matches(res)) {
    final URI href=toURI(res.getValue(ATTRIBUTE_NAME_HREF));
    final String scope=res.getValue(ATTRIBUTE_NAME_SCOPE);
    final String format=res.getValue(ATTRIBUTE_NAME_FORMAT);
    final String processingRole=res.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
    if (href != null && (scope == null || scope.equals(ATTR_SCOPE_VALUE_LOCAL)) && (format == null || format.equals(ATTR_FORMAT_VALUE_DITA)) && (processingRole == null || processingRole.equals(ATTR_PROCESSING_ROLE_VALUE_NORMAL))) {
      final URI file=stripFragment(href);
      Integer count=topicrefCount.containsKey(file) ? topicrefCount.get(file) : 0;
      count++;
      topicrefCount.put(file,count);
      if (count > 1) {
        final String copyTo=res.getValue(ATTRIBUTE_NAME_COPY_TO);
        if (copyTo == null) {
          final URI generatedCopyTo=generateCopyToTarget(href,count);
          final URI source=currentFile.resolve(file);
          final URI target=currentFile.resolve(stripFragment(generatedCopyTo));
          final URI relSource=getRelativePath(job.getInputDir().toURI(),source);
          final URI relTarget=getRelativePath(job.getInputDir().toURI(),target);
          copyToMap.put(relTarget,relSource);
          final AttributesImpl buf=new AttributesImpl(atts);
          XMLUtils.addOrSetAttribute(buf,ATTRIBUTE_NAME_COPY_TO,generatedCopyTo.toString());
          res=buf;
        }
      }
    }
  }
  getContentHandler().startElement(uri,localName,qName,res);
}