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I hope that there will be a radio button or a check box where Auto Save on Run can be disabled. Auto Save on Run is a bad idea. I often go into workflows and only need one report - so I break a bunch of connections to other reports, maybe I make some other small adhoc or one-off type changes and then Run the workflow. I get my one, maybe modified, report and close without saving. So the next time I open the workflow it's as it should be.
With Auto Save on Run - I'd have to undo everything I changed. What if it's not my workflow to be changing? If there is no option to turn it off: I'd have to make a copy of the workflow, open and make changes, then run, then close, then delete the workflow.
In general, you should never be saving unless it is a deliberate act performed by the user.