Github user sadhen commented on the issue:

    https://github.com/apache/zeppelin/pull/2539
  
    We deployed Zeppelin in K8S cluster, and are using volumes for persistence 
as you stated.
    
    A1. I will provide a solution later. A possible solution: mv the files in 
`conf/` if exists in `zeppelin.sh`.
    
    A2. Although `notebook` dir is version controlled, it is not relevant to 
this particular issue. Untracked files also lives well under version(git) 
controlled dir.
    
    -----
    
    The critical part is that files under `conf/` such as `shiro.ini` is part 
of the docker image and should be immutable. But `notebook-authorization.json` 
and `interpreter.json` is mutable and is changed in user activities. They are 
different in nature.
    
    The differences:
    1. `shiro.ini` is provided by admin and these two json is generated by 
Zeppelin itself
    2. `shiro.ini` should be part of the docker image, two docker images with 
totally different `shiro.ini` behaves in a totally different way. It is part of 
the deployment but the json files are record of user activities.
    
    Why should we keep these in different dirs?
    Since volumes are dirs. And the two json files should be kept in a volume.


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