>The Dr. Seuss books were banned not just by eBay but also by their publisher
I don't see the problem here. The copyright owner's no longer wish to distribute certain items in their intellectual property collection? So? I don't see people concerned that Disney isn't pulling "Song of the South" out of their vault, or isn't streaming it on Disney+.
What's the alternative you want? The government to FORCE artists to publish? FORCE Ebay to list these particular Dr. Seuss books? What the hell?? Isn't that worse?
>To reiterate, for me it seems that itunes and ebook reader generation of devices and applications don't seem to value custom directory organization.
Do you primarily or only use one computer or one os?
I'm on 3 different OSes regularly, over 5 different computers counting ones at work. For me, the effort to setup custom directory organization is a complete waste of time unless structure and tags can easily travel between computers, filesystems, and OSes.
Letting the app (Calibre for books, Mendeley Desktop for pdf's) organize however it wants lets me just clone the directory and preserve tags, which is actually what is important to me (or in the case of Mendeley, log in and sync documents/tags). I'm not a music listener at work or I'd just let an app organize that too if it syncs my tags.
I was like you, until my library grew to a certain size and I needed/wanted to organize it and display it better. Calibre lets me tag books, so I can pull them up by arbitrary categories which I can't EASILY pull off only using filesystem features. With Calibre I split my ebooks into two libraries (one for computer books, one for not computer books) and tag to my hearts content and requirements. I keep it simple to 2-3 tags for each book so I can later find my computer books that are "python, security" or my "reading challenge, crime/mystery, unread" books without dealing with extended attributes and the find command. Calibre also travels between linux, macos, and windows and so do the tags; unlike the filesystem where I'd get the joy of retagging all this stuff if I am on a different system (say, copy of my stuff on Windows means I have to retag with NTFS alternate data streams).
Same thing with pdf's - I used to keep a bunch of docs in my own subdir, until it got to be 1000+ pdf's and I discovered Mendeley Desktop and its tagging feature. Now I can find stuff much faster.
Same thing with my music collection, same thing my with photos.
Your needs may be minimal enough and your computer skills sufficient enough so that you get by with the filesystem, but I would venture to say the average user is much better off with an app/library method of organization. e.g., I can't fathom organizing a non-trivial photo collection via the filesystem only. I know I'm better off with the app/library method of organizing data, something I came to realize after my initial resistance.