Not sure I am following you....why do you want to use an invalid uri? the command can't run because of it...
Your goal is to provision the server.conf settings from the cli of the SH, right? or did I miss something?
There are both ./splunk add cluster-master and ./splunk edit cluster-master commands that do that...
http://docs.splunk.com/Documentation/Splunk/7.1.1/Indexer/ConfiguresearchheadwithCLI
if the goal is to not have to do this from the cli...why not just mount the proper configmap for server.conf? That is the "Kubernetes way" to accomplish this...way easier to manage and update, then having to go into the container....
On the configmaps - yeah I only use them for bootstrap configs (like this one)...want to add a new cluster? update config map and refresh the pod. all other configs are managed like the would be outside kube. I like that git provides me a repo for version control etc. Ideally this should keep things neat, not sure why it makes duplication for you?
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