Github user WangTaoTheTonic commented on the issue:

    https://github.com/apache/flink/pull/3335
  
    Hi Stephan,
    
    You may have a little misunderstanding about this change. It only controls 
directories with job id (generated using UUID), but not the configured root 
checkpoint directory.  I agree with you that the root directory should be 
created or changed permission when setup, but setup would not be aware of these 
directories with job ids, which are created in runtime.
    
    About Hadoop dependency, I admit I am using a convenient (let's say a hack 
way) to do the transition, as it need a bit more codes to do it standalone. I 
will change it if it's a problem :)


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