I'm still looking for the library solution that doesn't mess with whatever file/folder arrangement I choose. I find it very odd that this seems to be such a difficult deal to do in the ebook space, considering the vast array of picture/video and music managers that seem to have no problem with this.
I think Ubooquity is probably your best bet. But it's no longer maintained and has some issues with larger libraries due to how the library scan is implemented.
