Program: 100817
Project: 100817
Buggy source:
private void processParseResult(String currentFile){
  final Map<String,String> cpMap=reader.getCopytoMap();
  final Map<String,KeyDef> kdMap=reader.getKeysDMap();
  final Map<String,String> exKdMap=reader.getExKeysDefMap();
  exKeyDefMap.putAll(exKdMap);
  for (  final String file : reader.getNonCopytoResult()) {
    categorizeResultFile(file);
    updateUplevels(file);
  }
  for (  final String key : cpMap.keySet()) {
    final String value=cpMap.get(key);
    if (copytoMap.containsKey(key)) {
      final Properties prop=new Properties();
      prop.setProperty("String_Node_Str",value);
      prop.setProperty("String_Node_Str",key);
      logger.logWarn(MessageUtils.getMessage("String_Node_Str",prop).toString());
      ignoredCopytoSourceSet.add(value);
    }
 else {
      updateUplevels(key);
      copytoMap.put(key,value);
    }
  }
  schemeSet.addAll(reader.getSchemeRefSet());
  for (  final String key : kdMap.keySet()) {
    final KeyDef value=kdMap.get(key);
    if (keysDefMap.containsKey(key)) {
    }
 else {
      updateUplevels(key);
      keysDefMap.put(key,new KeyDef(value.keys,value.href,currentFile));
    }
    if (schemeSet.contains(currentFile)) {
      try {
        schemekeydef.writeStartElement("String_Node_Str");
        schemekeydef.writeAttribute("String_Node_Str",key);
        schemekeydef.writeAttribute("String_Node_Str",value.href);
        schemekeydef.writeAttribute("String_Node_Str",currentFile);
        schemekeydef.writeEndElement();
      }
 catch (      final SAXException e) {
        logger.logException(e);
      }
    }
  }
  hrefTargetSet.addAll(reader.getHrefTargets());
  hrefWithIDSet.addAll(reader.getHrefTopicSet());
  chunkTopicSet.addAll(reader.getChunkTopicSet());
  conrefTargetSet.addAll(reader.getConrefTargets());
  nonConrefCopytoTargetSet.addAll(reader.getNonConrefCopytoTargets());
  ignoredCopytoSourceSet.addAll(reader.getIgnoredCopytoSourceSet());
  subsidiarySet.addAll(reader.getSubsidiaryTargets());
  outDitaFilesSet.addAll(reader.getOutFilesSet());
  resourceOnlySet.addAll(reader.getResourceOnlySet());
  if (reader.getSchemeSet() != null && reader.getSchemeSet().size() > 0) {
    Set<String> children=null;
    children=this.schemeDictionary.get(currentFile);
    if (children == null) {
      children=new HashSet<String>();
    }
    children.addAll(reader.getSchemeSet());
    currentFile=currentFile.replace(WINDOWS_SEPARATOR,UNIX_SEPARATOR);
    this.schemeDictionary.put(currentFile,children);
    final Set<String> hrfSet=reader.getHrefTargets();
    for (    String f : hrfSet) {
      final String filename=f.replace(WINDOWS_SEPARATOR,UNIX_SEPARATOR);
      children=this.schemeDictionary.get(filename);
      if (children == null) {
        children=new HashSet<String>();
      }
      children.addAll(reader.getSchemeSet());
      this.schemeDictionary.put(filename,children);
    }
  }
}

Fixed version (ground truth):
private void processParseResult(String currentFile){
  final Map<String,String> cpMap=reader.getCopytoMap();
  final Map<String,KeyDef> kdMap=reader.getKeysDMap();
  final Map<String,String> exKdMap=reader.getExKeysDefMap();
  exKeyDefMap.putAll(exKdMap);
  for (  final String file : reader.getNonCopytoResult()) {
    categorizeResultFile(file);
    updateUplevels(file);
  }
  for (  final String key : cpMap.keySet()) {
    final String value=cpMap.get(key);
    if (copytoMap.containsKey(key)) {
      final Properties prop=new Properties();
      prop.setProperty("String_Node_Str",value);
      prop.setProperty("String_Node_Str",key);
      logger.logWarn(MessageUtils.getMessage("String_Node_Str",prop).toString());
      ignoredCopytoSourceSet.add(value);
    }
 else {
      updateUplevels(key);
      copytoMap.put(key,value);
    }
  }
  schemeSet.addAll(reader.getSchemeRefSet());
  for (  final String key : kdMap.keySet()) {
    final KeyDef value=kdMap.get(key);
    if (keysDefMap.containsKey(key)) {
    }
 else {
      updateUplevels(key);
      keysDefMap.put(key,new KeyDef(value.keys,value.href,currentFile));
    }
    if (schemeSet.contains(currentFile)) {
      try {
        schemekeydef.writeStartElement("String_Node_Str");
        schemekeydef.writeAttribute("String_Node_Str",key);
        if (value.href != null) {
          schemekeydef.writeAttribute("String_Node_Str",value.href);
        }
        schemekeydef.writeAttribute("String_Node_Str",currentFile);
        schemekeydef.writeEndElement();
      }
 catch (      final SAXException e) {
        logger.logException(e);
      }
    }
  }
  hrefTargetSet.addAll(reader.getHrefTargets());
  hrefWithIDSet.addAll(reader.getHrefTopicSet());
  chunkTopicSet.addAll(reader.getChunkTopicSet());
  conrefTargetSet.addAll(reader.getConrefTargets());
  nonConrefCopytoTargetSet.addAll(reader.getNonConrefCopytoTargets());
  ignoredCopytoSourceSet.addAll(reader.getIgnoredCopytoSourceSet());
  subsidiarySet.addAll(reader.getSubsidiaryTargets());
  outDitaFilesSet.addAll(reader.getOutFilesSet());
  resourceOnlySet.addAll(reader.getResourceOnlySet());
  if (reader.getSchemeSet() != null && reader.getSchemeSet().size() > 0) {
    Set<String> children=null;
    children=this.schemeDictionary.get(currentFile);
    if (children == null) {
      children=new HashSet<String>();
    }
    children.addAll(reader.getSchemeSet());
    currentFile=currentFile.replace(WINDOWS_SEPARATOR,UNIX_SEPARATOR);
    this.schemeDictionary.put(currentFile,children);
    final Set<String> hrfSet=reader.getHrefTargets();
    for (    String f : hrfSet) {
      final String filename=f.replace(WINDOWS_SEPARATOR,UNIX_SEPARATOR);
      children=this.schemeDictionary.get(filename);
      if (children == null) {
        children=new HashSet<String>();
      }
      children.addAll(reader.getSchemeSet());
      this.schemeDictionary.put(filename,children);
    }
  }
}