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This sounds a lot like a file system.

We can probably blame Apple for that; there are basically no good solutions to getting your comic / eBook collection on to the iPad.

No pun intended but the solution there is to buy an alternative tablet or device.

Agreeing with your main point: Apple does not provide a great solution for ebook library management and sync to iOS.

But there are good third-party options.

I recommend Kybook 3 on iOS for ebooks. OPDS sync from Calibre works well.

I only have occasional use for an iOS CBR/CBZ reader, but ComicFlow has worked for me, without any memorable problems.

That’s not an iPad problem, it’s an app problem. And there are tons of iOS apps that have solved that problem.

Nextcloud is exactly this.

My exact thought reading the link, there's plenty of ebook reader apps for nextcloud. It may even work out of the box, I'm not sure.

Same goes for most formats you can imagine, overseas family puts up lengthy holiday videos on my server and nearly everyone just watches it in the browser.