Program: 100789
Project: 100789
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.equalsIgnoreCase(attrValue)) {
      return;
    }
  }
 else   if (processLevel > 0) {
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equalsIgnoreCase(processStack.peek())) {
      return;
    }
  }
  AttributesImpl atts=null;
  if (MAP_TOPICREF.matches(attributes)) {
    String attValue=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.equalsIgnoreCase(scopeValue)) && (formatValue == null || ATTR_FORMAT_VALUE_DITA.equalsIgnoreCase(formatValue))) {
        final String ohref=attValue;
        final String copyToValue=atts.getValue(ATTRIBUTE_NAME_COPY_TO);
        if (!StringUtils.isEmptyString(copyToValue)) {
          attValue=copyToValue;
        }
        XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_OHREF,ohref);
        if (util.isVisited(attValue)) {
          attValue=SHARP + util.getIdValue(attValue);
        }
 else {
          String p=null;
          try {
            p=FileUtils.normalize(URLDecoder.decode(FileUtils.stripFragment(attValue),UTF8));
          }
 catch (          final UnsupportedEncodingException e) {
            throw new RuntimeException(e);
          }
          util.visit(p);
          if (p != null) {
            final File f=new File(dirPath,p);
            if (f.exists()) {
              topicParser.parse(p,dirPath);
              final String fileId=topicParser.getFirstTopicId();
              util.addId(attValue,fileId);
              final String firstTopicId=SHARP + fileId;
              if (util.getIdValue(attValue) != null) {
                attValue=SHARP + util.getIdValue(attValue);
              }
 else {
                attValue=firstTopicId;
              }
              XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_FIRST_TOPIC_ID,firstTopicId);
            }
 else {
              final String fileName=new File(dirPath,attValue).getAbsolutePath();
              logger.logError(MessageUtils.getInstance().getMessage("String_Node_Str",fileName).toString());
            }
          }
        }
      }
      XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_HREF,attValue);
    }
  }
  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.equalsIgnoreCase(attrValue)) {
      return;
    }
  }
 else   if (processLevel > 0) {
    processLevel++;
    if (ATTR_PROCESSING_ROLE_VALUE_RESOURCE_ONLY.equalsIgnoreCase(processStack.peek())) {
      return;
    }
  }
  AttributesImpl atts=null;
  if (MAP_TOPICREF.matches(attributes)) {
    String attValue=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.equalsIgnoreCase(scopeValue)) && (formatValue == null || ATTR_FORMAT_VALUE_DITA.equalsIgnoreCase(formatValue))) {
        final String ohref=attValue;
        final String copyToValue=atts.getValue(ATTRIBUTE_NAME_COPY_TO);
        if (!StringUtils.isEmptyString(copyToValue)) {
          attValue=copyToValue;
        }
        XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_OHREF,ohref);
        if (util.isVisited(attValue)) {
          attValue=SHARP + util.getIdValue(attValue);
        }
 else {
          String p=null;
          try {
            p=FileUtils.normalize(URLDecoder.decode(FileUtils.stripFragment(attValue),UTF8));
          }
 catch (          final UnsupportedEncodingException e) {
            throw new RuntimeException(e);
          }
          util.visit(p);
          if (p != null) {
            final File f=new File(dirPath,p);
            if (f.exists()) {
              topicParser.parse(p,dirPath);
              final String fileId=topicParser.getFirstTopicId();
              util.addId(attValue,fileId);
              if (FileUtils.getFragment(attValue) != null) {
                util.addId(FileUtils.stripFragment(attValue),fileId);
              }
              final String firstTopicId=SHARP + fileId;
              if (util.getIdValue(attValue) != null) {
                attValue=SHARP + util.getIdValue(attValue);
              }
 else {
                attValue=firstTopicId;
              }
              XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_FIRST_TOPIC_ID,firstTopicId);
            }
 else {
              final String fileName=new File(dirPath,attValue).getAbsolutePath();
              logger.logError(MessageUtils.getInstance().getMessage("String_Node_Str",fileName).toString());
            }
          }
        }
      }
      XMLUtils.addOrSetAttribute(atts,ATTRIBUTE_NAME_HREF,attValue);
    }
  }
  getContentHandler().startElement(uri,localName,qName,atts != null ? atts : attributes);
}