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`ghc-pkg check` reports non-existent include-dirs warnings

In the GHC 9.6.1 bindist ghc-pkg check reports that directory's package registration's include-dir field refers to a non-existent path:

$ ghc-pkg check
Warning: include-dirs: /nix/store/78g7mg8ni9y3ph1yvf7qxkiig32nb1wi-ghc-9.6.1-alpha1/lib/ghc-9.6.0.20230111/lib/../lib/x86_64-linux-ghc-9.6.0.20230111/directory-1.3.8.0/include doesn't exist or isn't a directory
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