Program: 26899
Project: 26899
Buggy source:
@Override protected void createColumnDefinitions(TypeElement typeElement){
  List<? extends Element> elements=manager.getElements().getAllMembers(typeElement);
  ColumnValidator columnValidator=new ColumnValidator();
  OneToManyValidator oneToManyValidator=new OneToManyValidator();
  for (  Element element : elements) {
    boolean isValidColumn=(allFields && (element.getKind().isField() && !element.getModifiers().contains(Modifier.STATIC) && !element.getModifiers().contains(Modifier.PRIVATE)&& !element.getModifiers().contains(Modifier.FINAL)));
    inheritedColumnMap.containsKey(element.getSimpleName().toString());
    if (element.getAnnotation(Column.class) != null || isValidColumn) {
      ColumnDefinition columnDefinition;
      if (element.getAnnotation(ForeignKey.class) != null) {
        columnDefinition=new ForeignKeyColumnDefinition(manager,element);
      }
 else {
        columnDefinition=new ColumnDefinition(manager,element);
      }
      if (columnValidator.validate(manager,columnDefinition)) {
        columnDefinitions.add(columnDefinition);
        mColumnMap.put(columnDefinition.columnName,columnDefinition);
        if (columnDefinition.isPrimaryKey) {
          primaryColumnDefinitions.add(columnDefinition);
        }
 else         if (columnDefinition instanceof ForeignKeyColumnDefinition) {
          foreignKeyDefinitions.add((ForeignKeyColumnDefinition)columnDefinition);
        }
 else         if (columnDefinition.isPrimaryKeyAutoIncrement) {
          autoIncrementDefinition=columnDefinition;
          hasAutoIncrement=true;
        }
        if (!columnDefinition.uniqueGroups.isEmpty()) {
          List<Integer> groups=columnDefinition.uniqueGroups;
          for (          int group : groups) {
            List<ColumnDefinition> groupList=columnUniqueMap.get(group);
            if (groupList == null) {
              groupList=new ArrayList<>();
              columnUniqueMap.put(group,groupList);
            }
            if (!groupList.contains(columnDefinition)) {
              groupList.add(columnDefinition);
            }
          }
        }
      }
    }
 else     if (element.getAnnotation(OneToMany.class) != null) {
      OneToManyDefinition oneToManyDefinition=new OneToManyDefinition(element,manager);
      if (oneToManyValidator.validate(manager,oneToManyDefinition)) {
        oneToManyDefinitions.add(oneToManyDefinition);
      }
    }
  }
}

Fixed version (ground truth):
@Override protected void createColumnDefinitions(TypeElement typeElement){
  List<? extends Element> elements=manager.getElements().getAllMembers(typeElement);
  ColumnValidator columnValidator=new ColumnValidator();
  OneToManyValidator oneToManyValidator=new OneToManyValidator();
  for (  Element element : elements) {
    boolean isValidColumn=(allFields && (element.getKind().isField() && !element.getModifiers().contains(Modifier.STATIC) && !element.getModifiers().contains(Modifier.PRIVATE)&& !element.getModifiers().contains(Modifier.FINAL)));
    inheritedColumnMap.containsKey(element.getSimpleName().toString());
    if (element.getAnnotation(Column.class) != null || isValidColumn) {
      ColumnDefinition columnDefinition;
      if (element.getAnnotation(ForeignKey.class) != null) {
        columnDefinition=new ForeignKeyColumnDefinition(manager,element);
      }
 else {
        columnDefinition=new ColumnDefinition(manager,element);
      }
      if (columnValidator.validate(manager,columnDefinition)) {
        columnDefinitions.add(columnDefinition);
        mColumnMap.put(columnDefinition.columnName,columnDefinition);
        if (columnDefinition.isPrimaryKey) {
          primaryColumnDefinitions.add(columnDefinition);
        }
 else         if (columnDefinition instanceof ForeignKeyColumnDefinition) {
          foreignKeyDefinitions.add((ForeignKeyColumnDefinition)columnDefinition);
        }
 else         if (columnDefinition.isPrimaryKeyAutoIncrement) {
          autoIncrementDefinition=columnDefinition;
          hasAutoIncrement=true;
        }
        if (!columnDefinition.uniqueGroups.isEmpty()) {
          List<Integer> groups=columnDefinition.uniqueGroups;
          for (          int group : groups) {
            List<ColumnDefinition> groupList=columnUniqueMap.get(group);
            if (groupList == null) {
              groupList=new ArrayList<>();
              columnUniqueMap.put(group,groupList);
            }
            if (!groupList.contains(columnDefinition)) {
              groupList.add(columnDefinition);
            }
          }
        }
      }
    }
 else     if (element.getAnnotation(OneToMany.class) != null) {
      OneToManyDefinition oneToManyDefinition=new OneToManyDefinition((ExecutableElement)element,manager);
      if (oneToManyValidator.validate(manager,oneToManyDefinition)) {
        oneToManyDefinitions.add(oneToManyDefinition);
      }
    }
  }
}