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I also use Calibre.
In Calibre's preferences you can set how you wish your books to be arranged. I opted for this
{authors}/{series} {series_index} - {title} - {authors}
Basically, it means that each author has his own folder and all books are in that folder.
Names of files are:
If a book is part of a series, the name of the series is placed in front, followed by the number in order, then goes "-", after that is the title of the book and author once again.
If the book is not part of a series then the name of the file starts with "-", the rest is the same.
As for indicating what you've read, there is the star rating system. Just put a star after you read it.
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