It seems my problem is related to this line in io.clj:
https://github.com/clojure/clojure/blob/f437b853adeaffc5cad9bb1e01e2355357a492c9/src/clj/clojure/java/io.clj#L60
(if (= "file" (.getProtocol u))
(as-file (escaped-utf8-urlstring->str
(.replace (.getFile u) \/ File/separatorChar)))
(throw (IllegalArgumentException. (str "Not a file: " u)))))
When running from the repl, .getProtocol returns "file", but when running from
an uberjar, .getProtocol returns "jar".
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