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Replying to
the problem online is that hyperlinks are not stable enough (target could vanish, go obsolete, get replaced), but the solution isn't to retreat to bad ports of dead-tree models... you need things inspired by transclusion (pull in a copy of enough of the cited ref)
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but you still do need to make a distinction between core text, and referential periphery matter. But it should exist as a sort of backdrop/margins fringe. Like if you wanted to preserve an impression in concrete, you'd carve out a slab around the impression.
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ie there's still a first class and second class citizen divide -- your content vs. referenced content. The flattened hyperlink model kinda dissolves that divide and then the core document decoheres. You don't want that. Unless you do...which you sometimes do
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actually, the idea of a "naked" reference with a very thin pointer as in "John Doe [1] argued that Vulcans are superior to Romulans because XYZ" is a product of scarcity because your private notes about [1] are too hard to expose in a useful way in a traditional research mode.
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Today, you'd want a fat/wrapped reference. The core text would be the same, but [1] would point to YOUR public note about the original text. It's like showing your source code. Show your "reading" of your source texts too.
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If it's a lazy ref where you didn't actually read it, but are citing it for political/social reasons (for eg. you expect the author to be a likely peer reviewer and want to flatter their conceit up front)... that's actually a social problem with peer review based production.
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Interestingly non-academic quasi-scholarly writing does not have this particular problem, though it has others. No kiss-ass citations. I hated those back when I was doing academic writing. I'm working on a whitepaper project now and it's refreshingly free of such imperatives.
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Replying to
Zotero / Mendelely are marginally better (but still not good). meta.org is very new and shiny but focused too much on discovery / feeds for working scientists, and not about managing your personal idiosyncratic pile of papers.
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