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Yes, there is a folder for each author. Then withing that a folder for each "title" and in that folder will contain all of the book formats.
I don't think that the file name matters... calibre will read the metadata in the ebook to get the title, author, etc. (Unless perhaps it is a text file.)
You might want to add a few folders at a time rather than do it in one full sweep. This will also let you create any tags or whatever if you want to match your current folder taxonomy.
BOb
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