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The docs do suggest that you should be seeing the RPD copied by EM to the publishing folder as well as the local repository folder on each node.
My understanding of it is that the Publishing folder is only used for distributing Online changes made to the RPD in a clustered environment although Nico says that it is used as the place from which the RPD is actually loaded on startup by all cluster members.
What happens if you try to edit the RPD online in your clustered environment; does anything get created in the publishing folder?
Are you even planning to even enable Online edits? Because if not the question could be moot.
Yes it should go to all the three locations, shared location and the local path of both the instances. but in my case, it is only copying the repository only to local instance of the bote, and not to the shared one. As per yoor suggession, I tried to make an online changes to the rep, but it only modified the instance from first instance only and not the rest.
To give an ans to your question, yes we allow online changes, not frequently we make changes in online mode but in rare cases, yes we do.