I ask the user. Every single time.
Sure, it's repetitive, and yes, the users get frustrated, but it's so fun to ask them the same questions every time (with confirmation for each question). The best part is when I ask for configuration options that my scripts don't use. ("Enter the distance from the Earth to the sun, in centimeters: ")
Or maybe I just use text files -- but that's a less interesting answer, so...
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