I've been browsing this thread for a while and would like to comment.
I think the issue here is how do you use calibre rather than a problem with the program itself.
I keep all my books organised by folder sorted by author on a portable harddrive for novels and by topic for reference books. I use calibre for converting and creating collections for both my wife's and my 505. When calibre is being used like this it is perfect.
In fact i have been looking for a program that will scan and reference my library folders rather than using calibre because of the limitations of calibre for organising books the way i want. In the mean time i'm using windows search and have the folders indexed which makes finding files very quick.
This I think is the salient point in my post.
Use calibre for managing libraries within the limitation of the reading device you are using but don't rely on it to be a complete library management application for a large library. Kovid has outlined on many occasions what he is willing to do with calibre and i for one am extremely grateful for the application which is miles better than the sony software and have donated as a result.
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