pnpm pack fails on 2.0–2.3 maintenance branches after running Deno 2.9 #1259

On the 2.0-maintenance through 2.3-maintenance branches, running any Deno 2.9.x command in the checkout rewrites the per-package node_modules/ directories that pnpm created. Afterwards, pnpm pack fails for packages that depend on another workspace package, because the workspace links are gone:

 ERR_PNPM_CANNOT_RESOLVE_WORKSPACE_PROTOCOL  Cannot resolve workspace protocol of dependency "@fedify/fedify" because this dependency is not installed. Try running "pnpm install".

I ran into this while verifying #1255 on 2.0-maintenance, where I wanted to pack @fedify/cfworkers and install the tarball with npm.

Cause

The root deno.json on these branches sets "nodeModulesDir": "auto". With that setting, Deno 2.9 sets up its own node_modules/.deno/ tree and relinks every workspace member's node_modules/ to it. The relinked directory no longer has the workspace dependencies pnpm linked there (@fedify/fedify in the case of @fedify/cfworkers) or some tool dependencies (tsdown, typescript). Older Deno releases leave the pnpm links alone.

I checked a fresh pnpm install --ignore-scripts of 2.0-maintenance followed by deno check packages/cfworkers/src/mod.ts with several Deno versions:

The pinned versions in mise.toml (2.7.7 on 2.0 and 2.1, 2.7.13 on 2.2, and 2.8.3 on 2.3) do not trigger this, so CI is not affected. It happens locally whenever a Deno 2.9 binary runs in a maintenance-branch checkout. For example, this can happen when a shell or editor still has main's Deno 2.9.7 on its PATH after switching branches, or when a global Deno is used outside mise.

main and 2.4-maintenance are not affected. Their deno.json was switched to "nodeModulesDir": "none" in fab1c07 together with the upgrade to Deno 2.9.5.

Steps to reproduce

1. Check out 2.0-maintenance (or 2.1–2.3) in a clean worktree.
2. Run pnpm install --ignore-scripts --frozen-lockfile.
3. Run deno check packages/cfworkers/src/mod.ts with Deno 2.9.x.
4. Run pnpm pack in packages/cfworkers/.

pnpm pack succeeds if you skip step 3.

Recovery is not obvious

A plain pnpm install restores the links, but in a normal checkout it also runs the root prepare script, which builds @fedify/vocab with deno task compile. If that deno is 2.9, the links are rewritten again right away, so pnpm install appears to have no effect. Running pnpm install --ignore-scripts, or making sure the pinned Deno is the one on PATH, recovers the checkout.

Possible fixes

• Backport "nodeModulesDir": "none" to 2.0-maintenance through 2.3-maintenance, if those branches still work without Deno managing node_modules/ (main changed it as part of a larger toolchain upgrade, so this needs checking).
• Alternatively, document that maintenance branches must be used with their pinned Deno version, and add a check (e.g., in mise run install) that fails early when the running Deno does not match mise.toml.