Program: 100648
Project: 100648
Buggy source:
private Attributes processAttributes(final Attributes atts){
  final String classValue=atts.getValue(ATTRIBUTE_NAME_CLASS);
  final AttributesImpl resAtts=new AttributesImpl(atts);
  for (int i=0; i < resAtts.getLength(); i++) {
    final String attrName=resAtts.getQName(i);
    String attrValue=resAtts.getValue(i);
    if (ATTRIBUTE_NAME_ID.equals(attrName)) {
      final String idValue=attrValue;
      if (TOPIC_TOPIC.matches(classValue)) {
        if (topicID.contains(attrValue)) {
          final String oldAttrValue=attrValue;
          attrValue=chunkFilenameGenerator.generateID();
          topicID.add(attrValue);
          final URI tmpValId=changeTable.get(setFragment(currentParsingFile,idValue));
          if (tmpValId != null && tmpValId.equals(setFragment(outputFile,idValue))) {
            changeTable.put(setFragment(currentParsingFile,idValue),setFragment(outputFile,attrValue));
          }
          final URI tmpVal=changeTable.get(currentParsingFile);
          if (tmpVal != null && tmpVal.equals(setFragment(outputFile,idValue))) {
            changeTable.put(currentParsingFile,setFragment(outputFile,attrValue));
          }
          currentParsingFileTopicIDChangeTable.put(oldAttrValue,attrValue);
        }
 else {
          topicID.add(attrValue);
        }
      }
    }
 else     if (ATTRIBUTE_NAME_HREF.equals(attrName)) {
      if (checkHREF(resAtts)) {
        URI relative=getRelativePath(outputFile,currentParsingFile);
        if (conflictTable.containsKey(outputFile.getPath())) {
          final URI realoutputfile=conflictTable.get(outputFile);
          relative=getRelativePath(realoutputfile,currentParsingFile);
        }
        if (attrValue.startsWith(SHARP)) {
          attrValue=relative + attrValue;
        }
 else         if (relative.toString().contains(SLASH)) {
          relative=setPath(relative,relative.getPath().substring(0,relative.getPath().lastIndexOf(SLASH)));
          attrValue=relative.resolve(attrValue).toString();
        }
      }
    }
    resAtts.setValue(i,attrValue);
  }
  if (TOPIC_TOPIC.matches(classValue) && resAtts.getValue(ATTRIBUTE_NAMESPACE_PREFIX_DITAARCHVERSION) == null) {
    addOrSetAttribute(resAtts,ATTRIBUTE_NAMESPACE_PREFIX_DITAARCHVERSION,DITA_NAMESPACE);
  }
  if (TOPIC_TOPIC.matches(classValue) && resAtts.getValue(XMLNS_ATTRIBUTE + "String_Node_Str" + DITA_OT_PREFIX) == null) {
    addOrSetAttribute(resAtts,XMLNS_ATTRIBUTE + "String_Node_Str" + DITA_OT_PREFIX,DITA_OT_NS);
  }
  return resAtts;
}

Fixed version (ground truth):
private Attributes processAttributes(final Attributes atts){
  final String classValue=atts.getValue(ATTRIBUTE_NAME_CLASS);
  final AttributesImpl resAtts=new AttributesImpl(atts);
  for (int i=0; i < resAtts.getLength(); i++) {
    final String attrName=resAtts.getQName(i);
    String attrValue=resAtts.getValue(i);
    if (ATTRIBUTE_NAME_ID.equals(attrName)) {
      final String idValue=attrValue;
      if (TOPIC_TOPIC.matches(classValue)) {
        if (topicID.contains(attrValue)) {
          final String oldAttrValue=attrValue;
          attrValue=chunkFilenameGenerator.generateID();
          topicID.add(attrValue);
          final URI tmpValId=changeTable.get(setFragment(currentParsingFile,idValue));
          if (tmpValId != null && tmpValId.equals(setFragment(outputFile,idValue))) {
            changeTable.put(setFragment(currentParsingFile,idValue),setFragment(outputFile,attrValue));
          }
          final URI tmpVal=changeTable.get(currentParsingFile);
          if (tmpVal != null && tmpVal.equals(setFragment(outputFile,idValue))) {
            changeTable.put(currentParsingFile,setFragment(outputFile,attrValue));
          }
          currentParsingFileTopicIDChangeTable.put(oldAttrValue,attrValue);
        }
 else {
          topicID.add(attrValue);
        }
      }
    }
 else     if (ATTRIBUTE_NAME_HREF.equals(attrName)) {
      if (checkHREF(resAtts)) {
        URI relative=getRelativePath(outputFile,currentParsingFile);
        if (conflictTable.containsKey(outputFile)) {
          final URI realoutputfile=conflictTable.get(outputFile);
          relative=getRelativePath(realoutputfile,currentParsingFile);
        }
        if (attrValue.startsWith(SHARP)) {
          attrValue=relative + attrValue;
        }
 else         if (relative.toString().contains(SLASH)) {
          relative=setPath(relative,relative.getPath().substring(0,relative.getPath().lastIndexOf(SLASH)));
          attrValue=relative.resolve(attrValue).toString();
        }
      }
    }
    resAtts.setValue(i,attrValue);
  }
  if (TOPIC_TOPIC.matches(classValue) && resAtts.getValue(ATTRIBUTE_NAMESPACE_PREFIX_DITAARCHVERSION) == null) {
    addOrSetAttribute(resAtts,ATTRIBUTE_NAMESPACE_PREFIX_DITAARCHVERSION,DITA_NAMESPACE);
  }
  if (TOPIC_TOPIC.matches(classValue) && resAtts.getValue(XMLNS_ATTRIBUTE + "String_Node_Str" + DITA_OT_PREFIX) == null) {
    addOrSetAttribute(resAtts,XMLNS_ATTRIBUTE + "String_Node_Str" + DITA_OT_PREFIX,DITA_OT_NS);
  }
  return resAtts;
}