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I just quickly browsed this thread, and apart from various philosophical complaints, I have yet to see one concrete use case that the calibre folder structure hampers. I may have missed it in my quick perusal, if so, please repost.
Speaking as a software developer philosophical complaints are not very motivating, use cases are.
So far the only concrete limitation of the calibre folder structure I know of is that it can get slow on windows because windows does not like large numbers of nodes in a single directory.
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