Program: 125634
Project: 125634
Buggy source:
public void addOrUpdateItem(Item item,boolean fromMigration){
  if (!loaded) {
    loadRelations();
  }
  if (item == null) {
    return;
  }
  boolean relationsModified=true;
  Relation relation=new Relation();
  relation.setId(item.getProperty().getId());
  relation.setType(getTypeFromItem(item));
  relation.setVersion(item.getProperty().getVersion());
  Set<Relation> oldProjectRelations=null;
  if (currentProjectItemsRelations.containsKey(relation)) {
    oldProjectRelations=new HashSet<Relation>(currentProjectItemsRelations.get(relation));
    currentProjectItemsRelations.get(relation).clear();
  }
  clearItemsRelations(item);
  final Map<Relation,Set<Relation>> itemRelations=getRelatedRelations(item);
  IItemRelationshipHandler[] itemRelationshipHandlers=RelationshipRegistryReader.getInstance().getItemRelationshipHandlers();
  for (  IItemRelationshipHandler handler : itemRelationshipHandlers) {
    Map<Relation,Set<Relation>> relations=handler.find(item);
    mergeRelationship(itemRelations,relations);
  }
  if (oldProjectRelations != null) {
    Set<Relation> newProjectRelations=currentProjectItemsRelations.get(relation);
    if (oldProjectRelations.size() == newProjectRelations.size()) {
      relationsModified=false;
      for (      Relation newRelation : newProjectRelations) {
        if (!oldProjectRelations.contains(newRelation)) {
          relationsModified=true;
          break;
        }
      }
    }
    if (!relationsModified) {
      currentProjectItemsRelations.get(relation).addAll(oldProjectRelations);
    }
  }
  if (relationsModified && !modified) {
    modified=true;
  }
  if (!fromMigration && modified) {
    saveRelations();
  }
}

Fixed version (ground truth):
public void addOrUpdateItem(Item item,boolean fromMigration){
  if (!supportRelation(item)) {
    return;
  }
  if (!loaded) {
    loadRelations();
  }
  if (item == null) {
    return;
  }
  boolean relationsModified=true;
  Relation relation=new Relation();
  relation.setId(item.getProperty().getId());
  relation.setType(getTypeFromItem(item));
  relation.setVersion(item.getProperty().getVersion());
  Set<Relation> oldProjectRelations=null;
  if (currentProjectItemsRelations.containsKey(relation)) {
    oldProjectRelations=new HashSet<Relation>(currentProjectItemsRelations.get(relation));
    currentProjectItemsRelations.get(relation).clear();
  }
  clearItemsRelations(item);
  final Map<Relation,Set<Relation>> itemRelations=getRelatedRelations(item);
  IItemRelationshipHandler[] itemRelationshipHandlers=RelationshipRegistryReader.getInstance().getItemRelationshipHandlers();
  for (  IItemRelationshipHandler handler : itemRelationshipHandlers) {
    Map<Relation,Set<Relation>> relations=handler.find(item);
    mergeRelationship(itemRelations,relations);
  }
  if (oldProjectRelations != null) {
    Set<Relation> newProjectRelations=currentProjectItemsRelations.get(relation);
    if (oldProjectRelations.size() == newProjectRelations.size()) {
      relationsModified=false;
      for (      Relation newRelation : newProjectRelations) {
        if (!oldProjectRelations.contains(newRelation)) {
          relationsModified=true;
          break;
        }
      }
    }
    if (!relationsModified) {
      currentProjectItemsRelations.get(relation).addAll(oldProjectRelations);
    }
  }
  if (relationsModified && !modified) {
    modified=true;
  }
  if (!fromMigration && modified) {
    saveRelations();
  }
}