Program: 100618
Project: 100618
Buggy source:
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes attributes) throws SAXException {
  final String attrValue=attributes.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
  if (attrValue != null) {
    processStack.push(attrValue);
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(attrValue)) {
      return;
    }
  }
 else   if (processLevel > 0) {
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(processStack.peek())) {
      return;
    }
  }
  AttributesImpl atts=null;
  if (MAP_TOPICREF.matches(attributes)) {
    URI attValue=toURI(attributes.getValue(ATTRIBUTE_NAME_HREF));
    if (attValue != null) {
      atts=new AttributesImpl(attributes);
      final String scopeValue=atts.getValue(ATTRIBUTE_NAME_SCOPE);
      final String formatValue=atts.getValue(ATTRIBUTE_NAME_FORMAT);
      if ((scopeValue == null || ATTR_SCOPE_VALUE_LOCAL.equals(scopeValue)) && (formatValue == null || ATTR_FORMAT_VALUE_DITA.equals(formatValue))) {
        final URI ohref=attValue;
        final URI copyToValue=toURI(atts.getValue(ATTRIBUTE_NAME_COPY_TO));
        if (copyToValue != null && !copyToValue.toString().isEmpty()) {
          attValue=copyToValue;
        }
        XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_OHREF,ohref.toString());
        if (util.isVisited(attValue)) {
          attValue=toURI(SHARP + util.getIdValue(attValue));
        }
 else {
          final URI p=stripFragment(attValue).normalize();
          util.visit(p);
          final File f=new File(dirPath,toFile(p).getPath());
          if (f.exists()) {
            topicParser.parse(toFile(p).getPath(),dirPath);
            final String fileId=topicParser.getFirstTopicId();
            util.addId(attValue,fileId);
            if (attValue.getFragment() != null) {
              util.addId(stripFragment(attValue),fileId);
            }
            final URI firstTopicId=toURI(SHARP + fileId);
            if (util.getIdValue(attValue) != null) {
              attValue=toURI(SHARP + util.getIdValue(attValue));
            }
 else {
              attValue=firstTopicId;
            }
            XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_FIRST_TOPIC_ID,firstTopicId.toString());
          }
 else {
            final URI fileName=dirPath.toURI().resolve(attValue);
            logger.error(MessageUtils.getInstance().getMessage("String_Node_Str",fileName.toString()).toString());
          }
        }
      }
      XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_HREF,attValue.toString());
    }
  }
  getContentHandler().startElement(uri,localName,qName,atts != null ? atts : attributes);
}

Fixed version (ground truth):
@Override public void startElement(final String uri,final String localName,final String qName,final Attributes attributes) throws SAXException {
  final String attrValue=attributes.getValue(ATTRIBUTE_NAME_PROCESSING_ROLE);
  if (attrValue != null) {
    processStack.push(attrValue);
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(attrValue)) {
      return;
    }
  }
 else   if (processLevel > 0) {
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equals(processStack.peek())) {
      return;
    }
  }
  AttributesImpl atts=null;
  if (MAP_TOPICREF.matches(attributes)) {
    URI attValue=toURI(attributes.getValue(ATTRIBUTE_NAME_HREF));
    if (attValue != null) {
      atts=new AttributesImpl(attributes);
      final String scopeValue=atts.getValue(ATTRIBUTE_NAME_SCOPE);
      final String formatValue=atts.getValue(ATTRIBUTE_NAME_FORMAT);
      if ((scopeValue == null || ATTR_SCOPE_VALUE_LOCAL.equals(scopeValue)) && (formatValue == null || ATTR_FORMAT_VALUE_DITA.equals(formatValue))) {
        final URI ohref=attValue;
        final URI copyToValue=toURI(atts.getValue(ATTRIBUTE_NAME_COPY_TO));
        if (copyToValue != null && !copyToValue.toString().isEmpty()) {
          attValue=copyToValue;
        }
        final URI absTarget=dirPath.toURI().resolve(attValue);
        XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_OHREF,ohref.toString());
        if (util.isVisited(absTarget)) {
          attValue=toURI(SHARP + util.getIdValue(absTarget));
        }
 else {
          final URI p=stripFragment(attValue).normalize();
          util.visit(absTarget);
          final File f=new File(stripFragment(absTarget));
          if (f.exists()) {
            topicParser.parse(toFile(p).getPath(),dirPath);
            final String fileId=topicParser.getFirstTopicId();
            util.addId(absTarget,fileId);
            if (attValue.getFragment() != null) {
              util.addId(stripFragment(absTarget),fileId);
            }
            final URI firstTopicId=toURI(SHARP + fileId);
            if (util.getIdValue(absTarget) != null) {
              attValue=toURI(SHARP + util.getIdValue(absTarget));
            }
 else {
              attValue=firstTopicId;
            }
            XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_FIRST_TOPIC_ID,firstTopicId.toString());
          }
 else {
            final URI fileName=dirPath.toURI().resolve(attValue);
            logger.error(MessageUtils.getInstance().getMessage("String_Node_Str",fileName.toString()).toString());
          }
        }
      }
      XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_HREF,attValue.toString());
    }
  }
  getContentHandler().startElement(uri,localName,qName,atts != null ? atts : attributes);
}