Program: 129603
Project: 129603
Buggy source:
@AfterClass public static void after() throws PersistenceException, CoreException {
  gefBot.closeAllShells();
  gefBot.saveAllEditors();
  gefBot.closeAllEditors();
  for (  ERepositoryObjectType epot : repositories) {
    System.out.print("String_Node_Str" + epot.getAlias() + "String_Node_Str"+ epot.getType());
    List<IRepositoryViewObject> ivos=ProxyRepositoryFactory.getInstance().getAll(epot);
    for (    IRepositoryViewObject ivo : ivos) {
      ProxyRepositoryFactory.getInstance().deleteObjectPhysical(ivo);
    }
    RepositoryManager.refresh(epot);
    RepositoryManager.refresh(ERepositoryObjectType.RECYCLE_BIN);
    gefBot.resetActivePerspective();
    Utilities.emptyRecycleBin();
  }
  Iterator<ERepositoryObjectType> it=repositoriesFolders.keySet().iterator();
  List<String> folderPaths;
  while (it.hasNext()) {
    ERepositoryObjectType key=it.next();
    folderPaths=repositoriesFolders.get(key);
    for (    String path : folderPaths) {
      IFolder folder=project.getFolder(key.getFolder() + "String_Node_Str" + path);
      if (folder.exists()) {
        System.out.println("String_Node_Str" + folder.exists());
        folder.delete(true,false,null);
      }
      project.refreshLocal(IResource.DEPTH_INFINITE,null);
    }
  }
  gefBot.resetActivePerspective();
  repositories.clear();
}

Fixed version (ground truth):
@AfterClass public static void after() throws PersistenceException, CoreException {
  gefBot.closeAllShells();
  gefBot.saveAllEditors();
  gefBot.closeAllEditors();
  IWorkspace workspace=ResourcesPlugin.getWorkspace();
  IWorkspaceRunnable operation=new IWorkspaceRunnable(){
    public void run(    IProgressMonitor monitor){
      for (      ERepositoryObjectType epot : repositories) {
        System.out.println("String_Node_Str" + epot.getAlias() + "String_Node_Str"+ epot.getType());
        final ProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
        List<IRepositoryViewObject> ivos=null;
        try {
          ivos=factory.getAll(epot);
        }
 catch (        PersistenceException e1) {
          e1.printStackTrace();
        }
        if (ivos != null) {
          for (          final IRepositoryViewObject ivo : ivos) {
            try {
              factory.deleteObjectLogical(ivo);
              RepositoryManager.refresh(epot);
              if (!repositoriesFolders.isEmpty()) {
                try {
                  Thread.sleep(ONE_MINUTE_IN_MILLISEC / 2);
                }
 catch (                InterruptedException e2) {
                  e2.printStackTrace();
                }
              }
              factory.deleteObjectPhysical(ivo);
            }
 catch (            PersistenceException e) {
              e.printStackTrace();
            }
catch (            BusinessException e) {
              e.printStackTrace();
            }
            RepositoryManager.refresh(epot);
          }
        }
      }
    }
  }
;
  workspace.run(operation,null);
  gefBot.resetActivePerspective();
  Utilities.emptyRecycleBin();
  IWorkspaceRunnable cleanup=new IWorkspaceRunnable(){
    public void run(    IProgressMonitor monitor){
      Iterator<ERepositoryObjectType> it=repositoriesFolders.keySet().iterator();
      List<String> folderPaths;
      while (it.hasNext()) {
        ERepositoryObjectType key=it.next();
        folderPaths=repositoriesFolders.get(key);
        for (        String path : folderPaths) {
          IFolder folder=project.getFolder(key.getFolder() + "String_Node_Str" + path);
          if (folder.exists()) {
            try {
              folder.delete(true,false,null);
            }
 catch (            CoreException e) {
              e.printStackTrace();
            }
          }
        }
      }
      try {
        project.refreshLocal(IResource.DEPTH_INFINITE,null);
      }
 catch (      CoreException e) {
        e.printStackTrace();
      }
      gefBot.resetActivePerspective();
    }
  }
;
  workspace.run(cleanup,null);
  repositories.clear();
  repositoriesFolders.clear();
}