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check_linkage wasn't warning about broken keg_only bottles because none of the audit_installed checks have been running for keg_only formulae. These checks have always been disabled for keg_only formulae, ever since keg_only formulae were first introduced in ee2b521 as checks kept getting added to the non-keg_only section of that block. But I cannot see any current reason they shouldn't be run. For keg_only formulae, we should still skip the checks for whether HOMEBREW_PREFIX/bin and HOMEBREW_PREFIX/sbin are in your PATH.