I think with this sort of thing, you have to consider the likelyhood of breakage.
If the nature of the application/configuration is relatively straightforward, and/or compatibility between the two versions is very strong, then I think the best thing to do is an automated migration. If on the other hand, breakage is very likely, then probably "halt and prompt" is best. An intermediate possibility, might be if the app has very good configuration file verification. Then you could do the automigration, VERIFY it, and then halt noisily if it fails verification. A post thought: in this case, I think you should always only copy; never remove. Worse case, 'mv' old config to config.migrated or something.
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