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The problem with that is that if one has — after substantial hand-editing — all of the nicely arranged files with nonduplicative filenames in Omnibus{1-6} created by group-merging volumes 1-6, and then volume 7 comes out, merging 7 into Omnibus{1-6} is, umm, nightmarish; and if there's ever volume 8... The editor doesn't show the subfolders, and one ends up with duplicate filenames that differ only by the invisible subfolders. And it's even worse when losing all meaningful filenames (as in a conversion from an azw source file). Conversely, if the filenames were made unique and not dependent upon subfolder references, flattening the epub makes the rest at least manageable (well, except when footnotes/endnotes are involved, but that's a huge gaping hole in epubs and the Kindle formats no matter what).
I suspect that the only way I'm getting that pony is in a bottle of glue.
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