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I think you may be getting a bit hung up on "directory's" and "folders"
Normally in Windows explorer I would applaud that, and indeed I can find anything in my System without using search, as its all organised exactly the way I want it.
However, Calibre does it's own organisation, its best you don't even look at the folders or directory's it creates, it doesn't really matter how it is storing your books, as long as you tag them and keep the meta data current.
"j b smith you will find as John B smith or John Baldy Smith or as j b smith"
For those I just find them in the list of authors, and rename them to J. B. Smith (Or John Baldy Smith) which ever takes your fancy. Then they are all organised correctly and only one entry exists for that author.
Indeed FN then LN is much better, that's the way I organize my Author names.
&&&& Secondary Authors, to me that just makes it easy to search for an Author, ie if its a book by A & B, then both of then will have an entry in the Author list, and if you only remember one of them you can still easily find the book you wanted.
Not sure if you asked any particular questions there, but hope above may of been of some help.
Oh, you may want to export as excel, and have a look through it that way, easy to do some searches that way, should you need to.
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