[anarcat]

This is actually what I want Calibre the most for. It sorts things in folders quite nicely.

I am one of those weirdos that really appreciated iTunes setting up my music by Artist/Album/Track.mp3 format back in the days... until I realized how much badly-tagged garbage I had in there at which point, yeah, I was upset. :p

But nowadays I just have books setup by Author/Book/book.epub and that ... works okay. I mean it's one way to sort things around. I am actually considering a fully flat structure now so that koreader can show me previews, and I think Calibre could allow that, as I can customize its naming patterns...

But yeah, it can be kind of annoying for software to rename files for you especially if you're not starting from scratch. But Calibre is the first thing I used to sync books on my ebook reader (a sony PRS-T2 i think!) so i did start from scratch and just kept going, so i didn't get many bad surprises, and it in fact forced me to keep my metadata clean to a certain extent (otherwise books end up in the wrong folder).