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I just whack the enter key ('Yes' is default). It only happens once per new epub (if it happens at all). I don't run into it all that often myself.
I wouldn't be opposed to "remembering" the decision (or making an environment variable to override it) IF we had a way to verify that the missing doctype was the only thing that was wrong. But I don't think we can easily determine that, and defaulting to 'yes' for any and all deformity seems dangerous to me. And defaulting to 'no' would disguise where the problem originated, in my opinion.
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