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Greetings! Whilst once again scavenging for parts in this fine .emacs.d (which has served as my template for years now) I discovered that setup-flycheck is not being loaded. It seems to have been removed accidentally, given that flycheck is being used for modes other than clojure. I thought I'd re-add the one missing line.
Details in my commit message: "Loading setup-flycheck was originally added in commit 0802ba4 but removed "for now" in commit f8c1baa."