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https://clojuredocs.org/clojure.core/require makes no mention of :exclude but this seems to work as it appears:

(require '[clojure.set :refer :all :exclude [join rename]])
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:exclude (and a few other clauses) are part of https://clojuredocs.org/clojure.core/refer and there is an example of :rename on the require page (another refer option). I guess it would be clearer if the require docstring mentioned the refer function and its options?
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Yes. Or at least said that require uses refer's options. But might as well list them.

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