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A lot of these uses are in archived repos, some are used intentionally (e.g. nextstrain.org tests), and some don't need changing (e.g. if the usage is the href of a link then it'll redirect). I think the only repos which actually need updates are: auspice, augur, cli, docs.nextstrain.org
These references are now outdated following nextstrain/nextstrain.org#811:
Not urgent, but it'd be good to have updated links at least on doc pages.
Repos to update
Repos that don't need update
Reasoning inline
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