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It sounds like a lot of trouble for a little-used feature (that even fewer run into trouble with) to me. You're the first to report an external editor adding an unmanifested file to an epub since the Open With feature was added back in 0.6.x or 0.7.x.
If we can come up with an easy way to prevent the problem, we surely will. But a considerable overhaul of the Open With feature code would quite frankly be more trouble than the feature is worth in my opinion.
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