Program: 74543
Project: 74543
Buggy source:
protected void _addConnections() throws TransformationException {
  for (  NamedObj replacement : _replacementToHost.keySet()) {
    if (!(replacement instanceof Port)) {
      continue;
    }
    Port replacementPort=(Port)replacement;
    Port hostPort=(Port)_replacementToHost.get(replacement);
    for (    Object replacementRelationObject : replacementPort.linkedRelationList()) {
      Relation replacementRelation=(Relation)replacementRelationObject;
      Relation hostRelation=(Relation)_replacementToHost.get(replacementRelation);
      if (!hostPort.linkedRelationList().contains(hostRelation)) {
        Entity hostPortContainer=(Entity)hostPort.getContainer();
        NamedObj hostContainer=hostRelation.getContainer();
        String moml="String_Node_Str" + hostPortContainer.getName() + "String_Node_Str"+ hostPort.getName()+ "String_Node_Str"+ hostRelation.getName()+ "String_Node_Str";
        MoMLChangeRequest request=new MoMLChangeRequest(this,hostContainer,moml);
        request.execute();
      }
    }
    if (replacementPort instanceof ComponentPort && hostPort instanceof ComponentPort) {
      ComponentPort replacementComponentPort=(ComponentPort)replacementPort;
      ComponentPort hostComponentPort=(ComponentPort)hostPort;
      for (      Object replacementRelationObject : replacementComponentPort.insideRelationList()) {
        Relation replacementRelation=(Relation)replacementRelationObject;
        Relation hostRelation=(Relation)_replacementToHost.get(replacementRelation);
        if (!hostComponentPort.insideRelationList().contains(hostRelation)) {
          NamedObj hostContainer=hostRelation.getContainer();
          String moml="String_Node_Str" + hostPort.getName() + "String_Node_Str"+ hostRelation.getName()+ "String_Node_Str";
          MoMLChangeRequest request=new MoMLChangeRequest(this,hostContainer,moml);
          request.execute();
        }
      }
    }
  }
}

Fixed version (ground truth):
protected void _addConnections() throws TransformationException {
  for (  NamedObj replacement : _replacementToHost.keySet()) {
    if (!(replacement instanceof Port)) {
      continue;
    }
    Port replacementPort=(Port)replacement;
    Port hostPort=(Port)_replacementToHost.get(replacement);
    for (    Object replacementRelationObject : replacementPort.linkedRelationList()) {
      Relation replacementRelation=(Relation)replacementRelationObject;
      Relation hostRelation=(Relation)_replacementToHost.get(replacementRelation);
      List<?> hostRelations=hostPort.linkedRelationList();
      if (hostRelation != null && !hostRelations.contains(hostRelation)) {
        Entity hostPortContainer=(Entity)hostPort.getContainer();
        NamedObj hostContainer=hostRelation.getContainer();
        String moml="String_Node_Str" + hostPortContainer.getName() + "String_Node_Str"+ hostPort.getName()+ "String_Node_Str"+ hostRelation.getName()+ "String_Node_Str";
        MoMLChangeRequest request=new MoMLChangeRequest(this,hostContainer,moml);
        request.execute();
      }
    }
    if (replacementPort instanceof ComponentPort && hostPort instanceof ComponentPort) {
      ComponentPort replacementComponentPort=(ComponentPort)replacementPort;
      ComponentPort hostComponentPort=(ComponentPort)hostPort;
      for (      Object replacementRelationObject : replacementComponentPort.insideRelationList()) {
        Relation replacementRelation=(Relation)replacementRelationObject;
        Relation hostRelation=(Relation)_replacementToHost.get(replacementRelation);
        if (!hostComponentPort.insideRelationList().contains(hostRelation)) {
          NamedObj hostContainer=hostRelation.getContainer();
          String moml="String_Node_Str" + hostPort.getName() + "String_Node_Str"+ hostRelation.getName()+ "String_Node_Str";
          MoMLChangeRequest request=new MoMLChangeRequest(this,hostContainer,moml);
          request.execute();
        }
      }
    }
  }
}