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Andyjenk - Many people only use calibre as a catalog - i.e. they don't keep their ebook 'format' files (.mobi, .pdf, .epub etc) in it's folders. If they do add them then its only as means of adding the book to the catalogue to extract any embedded metadata - they then remove the ebook format file, whilst leaving behind the 'catalogue entry'.
You will still get the author and book folders, but they'll only contain a cover.jpg and a metadata.opf. The first is so calibre can display them, the second is a backup of the metadata information that's used if the library database needs rebuilding. I've been using calibre for almost 3 years, I've never had to rebuild a database.
The Sort-xxxx columns are part of the Calibre furniture, it creates them automatically (there are set & forget preferences to control how), it can do hierarchical genres, and handles series quite neatly etc.
I can't think of anything that I could do in Excel or similar that I can't do in Calibre and more often than not its much easier in Calibre, and very rarely harder. But there are things I can do in Calibre that I wouldn't attempt to do in Excel - eg download metadata from sites like Goodreads, and covers from Google images.
By not adding the ebook files you will not have access to, or need, functions that operate on the ebook files - e.g. Conversion, Send to Device, Save to Disk, View and Edit.
As well as the GUI calibre also ships a rich set of
command line utilities, you may want to consider using them rather than, or in addition to, the GUI.
I suggest you use a subset of your library to create the 'catalogue' and start to explore calibres features. It can be a daunting program at first, but one of characteristics I like about Calibre is its consistency. After a while things I found that 'things' are almost invariably where I'd expect them to be, not parked in some obscure backwater like some programs. Another nice thing about Calibre is that if you don't use feature X there are usually no side effects - i.e. you don't lose access to something that has nothing to do with feature X.
BR