This really does seem like it should be a non-issue. The default MANIFEST.SKIP is usually smart enough, but if you find that you have to add some skips to it, look at ExtUtils::Manifest, where you can read everything you ever wanted to know about writing a MANIFEST and a MANIFEST.SKIP file.

For what its worth, I never use the make manifest command, but do find make distcheck to be useful. The former will just pull in all files in the build path that aren't skipped by either an explicit skip-file, or by the default one. I don't care for that. But the make distcheck command will just spit out a bunch of messages letting me know what files probably should be added to the manifest. In this case, keeping an up-to-date skip file just serves to silence the warnings.

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