Marginalia does not generally appear over the text on which it comments, because that would make both the text and the marginalia difficult to read. (Just look at the word - it's text that appears in the margins.)
So for practically all purposes, treating each note as an image which should be rendered to the side of a particular part of the dynamically-flowed text will solve the problem. This isn't that hard to do.
If someone is underlining parts of the text itself, that isn't independent of the flow of the text, and so it's harder to reflow. But I'm taking "notes" to mean commentary.
In the context of the reMarkable / this conversation, “notes” means whatever the user draws on the device with the stylus: underlining or circling or crossing-out words or drawing lines between them, drawing pictures or hand-writing in the margin or between lines or on the words, etc: whatever you would or could do with a physical book and a pen/pencil.
(A primary design goal of the reMarkable tablet is to be as similar to paper as possible, so (if I understood your suggestion correctly) telling users that their "notes" will be treated as images to be re-rendered to the side of the text, instead of where they put it—anywhere—would break the similarity, and apply only to a small subset of possible "notes", namely "commentary", as you said.)
I guess the affordances of the device influence what notes/annotations are likely to come into existence. On the Kindle, where IIRC input is through a keyboard (apart from highlighting), textual notes would be more common. On printed books and on the reMarkable (I'm even more "trigger-happy" on a reMarkable than on paper, probably because of undo and perfect erasing), annotation tends to be more free-form and varied, with more marks, scribbles, arrows etc, and a bit less text. Some of these annotations could also be understood and associated with corresponding text in principle, but it's not trivial. (Some examples of annotations from printed books: https://entropymag.org/writers-their-margin-notes/ )
I don't think so. The entire point of remarkable is to interact with the text. That is also How I have seen people use them at Uni. It's more like 99% of notes are tightly coupled to the text.
> So for practically all purposes, treating each note as an image which should be rendered to the side of a particular part of the dynamically-flowed text will solve the problem.
I don't think this is true. Even without underlines, which are common in notes, people place their notes based on a combination of the layout of the page and their personal preferences. I don't think it's possible to know, given one layout and note placement, how to place the note in a new layout.
It is also worth saying that many historic uses of marginalia (for example, commentary on the Tanakh) are also associated with particular parts of the text and could not be laid out as you are describing without losing intended meaning.
> It is also worth saying that many historic uses of marginalia (for example, commentary on the Tanakh) are also associated with particular parts of the text and could not be laid out as you are describing without losing intended meaning.
I don't understand this. What part of the intended meaning would be lost? I have a printing plate of part of a Chinese Buddhist text with traditional commentary attached, and it works almost identically to this modern HTML from Harvard Law Review ( https://harvardlawreview.org/2021/06/commonwealth-v-mccarthy... ) - there's an area on the page for the text, another area for the commentary, and symbols identify which comments apply to which parts of the text.
But the Harvard Law Review piece is exactly what I just described, except that the notes do not appear near the text to which they apply.
I can't read Hebrew either! But the way these books were typeset was to balance commentary with the text. For instance, you can see that the right page has a pretty substantial chunk of scripture in the middle (the central columns are scripture) and the left-handed one has only a couple of lines. This style doesn't have the central text with commentary as an optional note, it's a blending of text and commentary. So one "page" of text might be 100% Tanakh and the next might be 10% Tanakh and 90% commentary. Rendering either one of them as a contentious text stream (or even interwoven paragraphs) loses some of the authorial intent.
Obviously this is a pretty specific literary tradition and most marginalia works exactly like you describe, but I think it's worth remembering that our experience of text being one way is often more about the texts we've happened to encounter than any limits to the diversity of how humans have written.
The Chinese religious text looks basically the same as the right-hand page. It's surrounded by commentary on three sides instead of four sides, but that is a minor difference.
The left-hand page is obviously different, but it's not clear to me how much I should think of it as text and how much I should think of it as artwork / talismans.
Anyway, I agree that the commentary is presented as being at least as important as the text, but I don't see that as contradicting what I was describing above.
> So one "page" of text might be 100% Tanakh and the next might be 10% Tanakh and 90% commentary.
This style is also common in contemporary legal documents. (I searched briefly earlier for a good example and didn't find one.) A page will usually not be 90% footnotes, but it's not so rare for a page to be more than 50% footnotes. I think this is a pretty natural outcome of the fact that some parts of any text attract much more commentary than other parts. Despite the very high volume of footnote material in these documents, though, they are always presented in a manner that suggests the text comes first and the footnotes come second in importance. For example, the footnote to a particular bit of text may not all occur on the same page as the text it footnotes.
I would argue that the difference between the religious texts and contemporary legal briefs is that the commentary really is more important than the text in the first case, and really isn't in the second case. The religious texts have been preserved for so long that they don't have much meaning left independent of the interpretive tradition that the commentary provides.
But your own personal notes on something you've read are unlikely to be as centrally important as the accumulated interpretive tradition associated with a multi-thousand-year-old text. If you wrote it in the margin initially, keeping it in the margin seems fairly safe. That commentary you see printed around the scripture on the right-hand page didn't come from the book owner.
Honestly, for marginalia I would love it if you could just insert blank notes pages within pdfs and write on them! Also that you could read the pdf with those notes pages enabled/disabled, and easily copy/move them to a separate document later.
So for practically all purposes, treating each note as an image which should be rendered to the side of a particular part of the dynamically-flowed text will solve the problem. This isn't that hard to do.
If someone is underlining parts of the text itself, that isn't independent of the flow of the text, and so it's harder to reflow. But I'm taking "notes" to mean commentary.