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A `runtime:` specifier (e.g. node from `devEngines.runtime` or `pnpm runtime set`) round-trips to `devEngines.runtime`, which only recognizes the `runtime:` protocol. Under `catalogMode` strict/prefer the auto-save loop promoted it into a catalog and rewrote the manifest entry to `catalog:`, which broke that round-trip and stranded it in `devDependencies`. Skip `runtime:` specifiers in that loop.