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There have been several posts of varying civility from people who don't like the folder structure. Yours is an excellent example of one of the good ones (polite etc.)
Calibre copies (not moves) the items into its own database. The internal library folder structure is part of that database. Your original books are left where they are. This isn't going to change anytime soon.
Those who care about folder structure either accept the duplication and continue to use calibre (space is very cheap, after all), or they find another solution. What that solution might be, I don't know. I can say that this forum is almost certainly not the right place to discuss alternatives to calibre. One of the other mobileread forums might work better.
Good luck in your quest.
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