The durable way to manage PDF and EPUB notes locally is to store source documents, reading positions, annotations, long-form notes, and search indexes as distinct data that remains connected by stable document identities and locations. Folders classify files; location, structure, and exportability determine whether you can recover the knowledge later.
PDFs are already strong at expression and rendering stability. What still feels underdeveloped is how annotations participate in learning, research, and knowledge work afterward.
PDFs have never been a format that nobody complains about.
But I increasingly feel that many of those complaints miss the real problem.
I do not dislike PDFs. If anything, I think PDFs are still a remarkably strong document format. Their expressive range is rich, their layout is stable, and their rendering is consistent across devices. For papers, reports, court decisions, scanned books, and other layout-sensitive documents, that stability is not a flaw. It is one of the main reasons the format remains useful. Complex layout, charts, footnotes, formulas, and page relationships can all be preserved with reasonable fidelity. If the goal is to deliver content accurately to a reader, PDFs still do that job very well.