Dr_Manhattan comments on Hyperlinks and Less Wrong - Less Wrong Discussion
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Thanks for posting, I had the same thought (but not the same dedication and research backup to post about it myself).
I think footnotes with links would be a decent compromise; limit in-article links to explanations of terms readers might not know.
In general seems that links should not be an "green smatter overlay" which the article reads without, they should be explicit references (e.g. "and take a look at this article").
I actually literally read the wired article the day before I started exploring Less Wrong, a few months ago. I wonder if the article primed me to be particularly annoyed. But I think the issues exist regardless.