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Percentage read is probably the best way to go, but for many I suspect it is so "unbooklike" as to offend a significant segment. Personally, other than being able to refer back to something I'd just be happy with what chapter I'm in most of the time.
Didn't think I was even close as to the particulars of annotation math, I was just pointing out a possible method and that it had to be independent of font size and page constraints. So you're saying that annotations must also track which files they refer to or be stored as part of the files, as well as how many paragraphs and words in from the top of file they are. Reasonable enough.
I think some people are going to have to get used to the idea that every little feature they'd prefer is not necessarily model-able, or may just be too big a resource hog or take to long to execute while people are waiting. Granted there may be a way to beat most constraints if the engineer is willing/able to put enough brainsweat into doing it, but not always and you always have to trade one thing off for another -it's the main difference between dreaming and engineering...
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