Program: 138389
Project: 138389
Buggy source:
private void handlePropertiesFile(File propFile,Map<File,File> folderMap,File parentFolder) throws PersistenceException, IOException {
  URI uri=URI.createFileURI(propFile.getAbsolutePath());
  Resource resource=resourceSet.getResource(uri,true);
  Property property=(Property)EcoreUtil.getObjectByType(resource.getContents(),PropertiesPackage.eINSTANCE.getProperty());
  if (property != null) {
    File targetFolder=folderMap.get(parentFolder);
    Item item=property.getItem();
    String connNameBofore=null;
    String connNameAfter=null;
    IPath path=new Path(item.getState().getPath());
    if (ProxyRepositoryFactory.getInstance().getFolderItem(ProjectManager.getInstance().getCurrentProject(),ERepositoryObjectType.getItemType(item),path) == null) {
      ProxyRepositoryFactory.getInstance().createFolder(ERepositoryObjectType.getItemType(item),path.removeLastSegments(1),path.lastSegment());
    }
    String connName=null;
    if (item instanceof ConnectionItem) {
      Connection conn=((ConnectionItem)item).getConnection();
      connNameBofore=conn.eResource().getURI().trimFileExtension().lastSegment();
      String version=property.getVersion();
      if (version == null) {
        version="String_Node_Str";
      }
      String label=conn.getName() + "String_Node_Str" + version;
      connNameAfter=label;
      File destItemFile=new Path(targetFolder.getAbsolutePath()).append(path).append(connNameAfter).addFileExtension(FactoriesUtil.ITEM_EXTENSION).toFile();
      File destPropFile=new Path(targetFolder.getAbsolutePath()).append(path).append(connNameAfter).addFileExtension(FactoriesUtil.PROPERTIES_EXTENSION).toFile();
      if (destItemFile.exists()) {
        int num=0;
        while (destItemFile.exists() || destPropFile.exists()) {
          connName=conn.getName() + String.valueOf(++num);
          connNameAfter=connName + "String_Node_Str" + version;
          destItemFile=new Path(destItemFile.getPath()).removeLastSegments(1).append(connNameAfter).addFileExtension(FactoriesUtil.ITEM_EXTENSION).toFile();
          destPropFile=new Path(destPropFile.getPath()).removeLastSegments(1).append(connNameAfter).addFileExtension(FactoriesUtil.PROPERTIES_EXTENSION).toFile();
        }
        conn.setName(connName);
        conn.setLabel(connName);
        property.setLabel(connName);
      }
      String relationPropPath=ReponsitoryContextBridge.getRootProject().getFullPath().append(new Path(destPropFile.getPath()).makeRelativeTo(this.getWorkspacePath())).toOSString();
      MetadataHelper.setPropertyPath(relationPropPath,conn);
    }
    if (isWorksapcePath()) {
      ProxyRepositoryFactory.getInstance().create(item,path,true);
    }
 else {
      connNameAfter=copyFile(targetFolder,propFile,property,path,connNameAfter,folderMap);
    }
    if (connNameBofore != null && connNameAfter != null) {
      getReplaceStringMap().put(connNameBofore,connNameAfter);
    }
  }
}

Fixed version (ground truth):
private void handlePropertiesFile(File propFile,Map<File,File> folderMap,File parentFolder) throws PersistenceException, IOException {
  URI uri=URI.createFileURI(propFile.getAbsolutePath());
  Resource resource=resourceSet.getResource(uri,true);
  Property property=(Property)EcoreUtil.getObjectByType(resource.getContents(),PropertiesPackage.eINSTANCE.getProperty());
  if (property != null) {
    File targetFolder=folderMap.get(parentFolder);
    Item item=property.getItem();
    String connNameBofore=null;
    String connNameAfter=null;
    IPath path=new Path(item.getState().getPath());
    if (ProxyRepositoryFactory.getInstance().getFolderItem(ProjectManager.getInstance().getCurrentProject(),ERepositoryObjectType.getItemType(item),path) == null) {
      ProxyRepositoryFactory.getInstance().createFolder(ERepositoryObjectType.getItemType(item),path.removeLastSegments(1),path.lastSegment());
    }
    String connName=null;
    if (item instanceof ConnectionItem) {
      Connection conn=((ConnectionItem)item).getConnection();
      connNameBofore=conn.eResource().getURI().trimFileExtension().lastSegment();
      String version=property.getVersion();
      if (version == null) {
        version="String_Node_Str";
      }
      String label=conn.getName() + "String_Node_Str" + version;
      connNameAfter=label;
      File destItemFile=new Path(targetFolder.getAbsolutePath()).append(path).append(connNameAfter).addFileExtension(FactoriesUtil.ITEM_EXTENSION).toFile();
      File destPropFile=new Path(targetFolder.getAbsolutePath()).append(path).append(connNameAfter).addFileExtension(FactoriesUtil.PROPERTIES_EXTENSION).toFile();
      if (destItemFile.exists()) {
        int num=0;
        while (destItemFile.exists() || destPropFile.exists()) {
          connName=conn.getName() + String.valueOf(++num);
          connNameAfter=connName + "String_Node_Str" + version;
          destItemFile=new Path(destItemFile.getPath()).removeLastSegments(1).append(connNameAfter).addFileExtension(FactoriesUtil.ITEM_EXTENSION).toFile();
          destPropFile=new Path(destPropFile.getPath()).removeLastSegments(1).append(connNameAfter).addFileExtension(FactoriesUtil.PROPERTIES_EXTENSION).toFile();
        }
        conn.setName(connName);
        conn.setLabel(connName);
        property.setLabel(connName);
      }
      String relationPropPath=ReponsitoryContextBridge.getRootProject().getFullPath().append(new Path(destPropFile.getPath()).makeRelativeTo(this.getWorkspacePath())).toOSString();
      MetadataHelper.setPropertyPath(relationPropPath,conn);
    }
    if (isWorksapcePath()) {
      ProxyRepositoryFactory.getInstance().create(item,path,true);
    }
 else {
      connNameAfter=copyFile(targetFolder,propFile,property,path,connNameAfter,connName,folderMap);
    }
    if (connNameBofore != null && connNameAfter != null) {
      getReplaceStringMap().put(connNameBofore,connNameAfter);
    }
  }
}