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How do I include .org.gpg files in my org-agenda-files? By default, it ignores them.

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Override org-agenda-file-regexp as shown to include .org.gpg files, then set org-agenda-files as usual.

(unless (string-match-p "\\.gpg" org-agenda-file-regexp)
  (setq org-agenda-file-regexp
        (replace-regexp-in-string "\\\\\\.org" "\\\\.org\\\\(\\\\.gpg\\\\)?"
                                  org-agenda-file-regexp)))

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