Hmmm... after reading this entire thread, I'm with Kovid here. The thread began with a question about indexing the books on this site, then moved to "what about a tool to organize/index MY books", and one suggestion was, "use Calibre, that's what it does".
To claim that Calibre discussion is off-topic, then, is silly. I very much like Calibre and think it might well be my book indexing/organization tool of choice. I understand the urge to write software, being a coder myself, but have you considered offering your SQL skills to Kovid?
Frankly, I don't care where the books are stored, as long as I can back them up. I want to find particular titles, sort my collection various ways, have a nice search mechanism, a color scheme or tagging scheme I can customize (original format, original source, on the Reader or not, already read, paper version only, etc.). If the best way to do that is to copy all your books to a central location, that's fine with me. I think Kovid's question, to paraphrase, "why do you care about folders?" is cogent. If the software lets you interact with the books, who cares what folder organization is used?
I'll be very interested in what you come up with, but I'm equally interested in existing tools.