Hi guys,
1st post, although I've read various threads while I was considering which reader to get and while I was setting up—thanks for all the help this forum has given

.
Just thought I can give a use case for an ebook manager to
not copy books, and perhaps give Kovid more incentive to consider implementing the feature:
I'm in the middle of my Masters degree and got an ebook reader to manage all the various resources, datasheets, reports, etc that I read. I also have a few novels, and non-Masters-related material on it for reading in my free time.
At the beginning of my Masters, I got a Dropbox account to do automatically back up all the stuff related to my research, and Dropbox insists on using its own folder structure. No biggie, since I only just started, so I copied everything over. However, now that I need to transfer all those things to the reader, I don't really feel like making and maintaining a second copy.
In my Dropbox folder are things that the reader can't handle properly: HTML archives, Word/Excel/Powerpoint documents, proprietary data files, video files, etc. Many PDFs and ePub files are also derived from those proprietary documents, and I'd really prefer to keep those together rather than make a new folder full of assorted documents purely so I can transfer them to the reader. So establishing the Calibre Library in the Dropbox isn't a solution either. Having Calibre manage all my books would be nice, yes, but when I already have an established folder structure, I'd rather keep that intact.
The more I read up on it, the more I realise I only want a way to easily sync documents and make collections on my PRS-T1, instead of a full-blown manager. Unfortunately that kind of software doesn't seem to exist, and Calibre is the closest thing I can find.
The comparison with iTunes is quite apt, actually. In the early days, iTunes couldn't handle a lot of the files that came with MP3 albums (eg cover scans, insert notes, lossless files, interactive what-nots), and even now, iTunes is being asked to handle many other files (iBooks, movie files, apps, photos, contacts, etc). I think Apple provided for file linking simply because they realise not everyone would use iTunes in the same way, and wanted it to be flexible.
Sorry for the long post, but a complex issue requires a detailed explanation