Program: 137488
Project: 137488
Buggy source:
@Override protected void run(){
  try {
    for (    ItemRecord record : fRecords) {
      if (fMonitor.isCanceled()) {
        break;
      }
      Map<IPath,IPath> toImportMap=mapping(record);
      fMonitor.subTask("String_Node_Str" + record.getName());
      if (record.isValid()) {
        log.info("String_Node_Str" + record.getFile().getAbsolutePath());
        IRepositoryViewObject object=record.getConflictObject();
        boolean isDelete=true;
        ModelElement modEle=record.getElement();
        if (object != null) {
          if (isIndicatorDefinition(modEle)) {
            if (isDQRule(modEle)) {
              if (isParserRule(modEle)) {
                mergeParserRule(record,(TDQBusinessRuleItem)object.getProperty().getItem());
                isDelete=false;
              }
 else               if (isWhereRule(modEle)) {
              }
            }
 else             if (isMatchRuleDefinition(modEle)) {
            }
 else {
              mergeSystemIndicator(record,(TDQIndicatorDefinitionItem)object.getProperty().getItem());
              isDelete=false;
            }
          }
 else           if (isPattern(modEle)) {
            mergePattern(record,(TDQPatternItem)object.getProperty().getItem());
            isDelete=false;
          }
        }
        if (isDelete) {
          for (          IPath resPath : toImportMap.keySet()) {
            IPath desPath=toImportMap.get(resPath);
            ResourceSet resourceSet=ProxyRepositoryFactory.getInstance().getRepositoryFactoryFromProvider().getResourceManager().resourceSet;
synchronized (resourceSet) {
              write(resPath,desPath);
              allCopiedFiles.add(desPath.toFile());
            }
          }
        }
      }
 else {
        for (        String error : record.getErrors()) {
          log.error(error);
        }
      }
      fMonitor.worked(1);
    }
    finish(fRecords,fMonitor);
  }
 catch (  Exception e) {
    log.error(e,e);
  }
}

Fixed version (ground truth):
@Override protected void run(){
  try {
    for (    ItemRecord record : fRecords) {
      if (fMonitor.isCanceled()) {
        break;
      }
      Map<IPath,IPath> toImportMap=mapping(record);
      fMonitor.subTask("String_Node_Str" + record.getName());
      if (record.isValid()) {
        log.info("String_Node_Str" + record.getFile().getAbsolutePath());
        IRepositoryViewObject object=record.getConflictObject();
        boolean isDelete=true;
        ModelElement modEle=record.getElement();
        if (object != null) {
          if (isIndicatorDefinition(modEle)) {
            if (isDQRule(modEle)) {
              if (isParserRule(modEle)) {
                mergeParserRule(record,(TDQBusinessRuleItem)object.getProperty().getItem());
                isDelete=false;
              }
 else               if (isWhereRule(modEle)) {
              }
            }
 else             if (isMatchRuleDefinition(modEle)) {
            }
 else {
              mergeSystemIndicator(record,(TDQIndicatorDefinitionItem)object.getProperty().getItem());
              isDelete=false;
            }
          }
 else           if (isPattern(modEle)) {
            mergePattern(record,(TDQPatternItem)object.getProperty().getItem());
            isDelete=false;
          }
 else {
            ProxyRepositoryFactory.getInstance().deleteObjectPhysical(object);
          }
        }
        if (isDelete) {
          for (          IPath resPath : toImportMap.keySet()) {
            IPath desPath=toImportMap.get(resPath);
            ResourceSet resourceSet=ProxyRepositoryFactory.getInstance().getRepositoryFactoryFromProvider().getResourceManager().resourceSet;
synchronized (resourceSet) {
              write(resPath,desPath);
              allCopiedFiles.add(desPath.toFile());
            }
          }
        }
      }
 else {
        for (        String error : record.getErrors()) {
          log.error(error);
        }
      }
      fMonitor.worked(1);
    }
    finish(fRecords,fMonitor);
  }
 catch (  Exception e) {
    log.error(e,e);
  }
}