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Applying search head cluster bundle not removing old directories feature or bug?

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Dear all, I am experiencing follwoing issue with Splunk 6.3.0 on linux machines: Before setting up a search head cluster we have had a script contained in our app within the "bin" folder to synchronise our lookup tables. After setting up the cluster this functionality is no longer required. I therefore removed the bin folder completely from our app and redistributed the app to our deployer. Then I applied the shcluster bundle via command to the sh. Now I see that on all search heads the old bin folder is still there... On the deployer I was able to verify that the folder no longer is there. I tought that maybe the command /opt/splunk/splunk/bin/splunk apply shcluster-bundle --answer-yes -target : -preserve-lookups true -auth : would also preserve old folder so I removed the parameter -preserve-lookups untortunately this didn't help either. Next I re-created the bin folder and only placing a README file there. Hopeing that this would overwritte the existing and no longer needed script on the search heads... I can still find the script on the search head instances. Is this a wanted feature or is this possibly an error in the distribution mechanism? Did someone experience the same? The only workaround I can think of now is to place a script within the apps for the sh instances to clean-up on the instance direclty and restarting those... Any other ideas or hints are greatly appreciated.

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