This file is indexed.

/etc/emacs/site-start.d/50lilypond-data.el is in lilypond-data 2.18.2-4.1.

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(autoload 'LilyPond-mode "lilypond-mode" nil t)
(setq auto-mode-alist (cons '("\\.ly$" . LilyPond-mode) auto-mode-alist))
(add-hook 'LilyPond-mode-hook (lambda () (turn-on-font-lock)))