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Definitely a bug when you run a script and then try to click the drop down and choose another file. This causes the editor to detect a change and the filename gets changed to the original with a *. At that point if you run or click save you will overwrite. But the process is pretty manual in that you have to select a file from that drop down.
I kind of liked the ability to see the files that we drilled into during the test but I couldn't figure out a way to disable the change callback during this change.