manifest.yaml must actually exist on disk at publish time. schema.json, permissions.yaml, and dependencies.yaml each have an unambiguous empty default and are filled in automatically when absent — a minimal skill isn’t forced to carry placeholder files just to say “none of this applies.”
The entrypoint file the manifest names is packaged alongside the four documents whenever it exists, but its format is never validated as structured data — that’s entirely runtime-family-dependent. README.md, changelog.md, tests/, and examples/ are part of the canonical layout but are not currently packaged.