I recently learned that I can use the script console to run groovy scripts 
to modify items in the model.

Specifically, I would like to add, change and remove slave node labels via 
a script.

I can make a script like this for example:

hudson.model.Hudson.instance.slaves.each { slave -> 
  out.print("Slave  $slave.nodeName : Labels: $slave.labelString")
  slave.setLabelString(slave.labelString + " " + "operational")
  out.println("   --> New labels: $slave.labelString")}

Now how do I persist this change to disk?

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