Dependency graph support for two-document pnpm-lock.yaml (pnpm 12)

[blimmer]

🏷️ Discussion Type

Bug

💬 Feature/Topic Area

Supply chain security

Discussion Details

The 2026-10-20 changelog post lists a known limitation: when pnpm writes pnpm-lock.yaml as two YAML documents, the dependency graph doesn't detect any dependencies in that file, so Dependabot alerts and security updates aren't created for them. The post says you're working on support.

Is there a public place to follow that work? The only thread I've found is dependabot/dependabot-core#15904, but Dependabot version updates already read the format (dependabot/dependabot-core#15968), and the dependency graph parser doesn't live in that repo. Maybe this ticket can be the public tracker?

pnpm 12 writes the two-document layout when package.json pins pnpm and pmOnFail isn't ignore. pnpm documented how to read it in pnpm/pnpm.io#895: read every document and use the last one.

Today, we have to set pmOnFail: ignore to keep the lockfile to one document, which also turns off pnpm's version check. Corepack used to enforce the pinned version for us, but Node.js 25 and later no longer ship it. Without Corepack, pnpm switching itself to the pinned version (pmOnFail: download, the default) is what keeps everyone on the same version, and every value other than ignore writes the two-document lockfile. Until the dependency graph reads that format, we have to choose between Dependabot alerts and a consistent pnpm version.

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[v-robaiken]

@blimmer Thanks for raising this. The dependency graph now reads two-document pnpm-lock.yaml files, and existing graphs may need a manual refresh to pick up the fix. I've posted the details and refresh steps on dependabot/dependabot-core#15904 (comment).

Once your graph has refreshed and your dependencies show up correctly, you should be able to drop the pmOnFail: ignore workaround.

[blimmer]

Thanks, LGTM!