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/etc/emacs/site-start.d/60agda-stdlib.el is in agda-stdlib 0.11-1.

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;; This will be overwritten if the user customises the agda2-include-dirs
;; variable in his/her own session. But that is probably the intended behaviour
;; anyway.

(setq agda2-include-dirs '("." "/usr/share/agda-stdlib"))