Enable check_repository_references conditionally

Enable check_repository_references when HOMEBREW_PREFIX == HOMEBREW_REPOSITORY.

Co-authored-by: Mike McQuaid <mike@mikemcquaid.com>

Library/Homebrew/formula_cellar_checks.rb

@@ -210,6 +210,7 @@ module FormulaCellarChecks
   end
 
   def check_repository_references(prefix)
+    return if HOMEBREW_PREFIX != HOMEBREW_REPOSITORY
     return unless prefix.directory?
 
     keg = Keg.new(prefix)