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Hi,
OK, you have plenty of things you want to do here.
First, it is not a problem to store author name in form of SURNAME, FIRSTNAME, if you want to do it. Also, if you already have books on your library in form FIRSTNAME SURNAME, you can run mass convert to switch them over. I got excellent instructions for that from this forum, I will try to find out the thread.
Second, when you want to import your books, it is possible to modify import options so that the import automatically picks up the author right. You just need to sort the books in different folders (folder1 to books with author in form FIRSTNAME SURNAME, and folder2 to books with author in form SURNAME, FIRSTNAME). Then just import the books with certain option so that your results will be right.
It is even possible to import books with the Series name and series numbers. You will need to modify the import regexp. There is instructions somewhere for that too.
Regarding for the disk folder structure, it will automatically be so how Calibre wants it - it is using the directory structure as its database, so you cannot mess around of it manually. Calibre creates own folder for each author, but book series are not getting folders.
After I started to use calibre, I have never bothered to look the disk structure. It is much easier to find what I am looking for with calibre than directly from file manager.
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