pnpm can report up-to-date while node_modules link metadata is broken, causing missing local binaries

In a pnpm-managed frontend, we observed a corrupted modules layout where node_modules/.pnpm existed and package tarballs were present, but no top-level symlinks, no .bin, and no .modules.yaml. This made pnpm run dev fail with sh: vite: command not found even though vite was in devDependencies. Running pnpm install (and even --force) returned quickly as up-to-date and did not relink. Removing node_modules and reinstalling rebuilt link metadata and restored binaries. Verified 2026-05 on macOS with pnpm 11.

If pnpm run/pnpm exec cannot find a known devDependency binary (for example vite) but .pnpm/ exists, verify whether node_modules/.bin, top-level package symlinks, and .modules.yaml are missing. Recover by deleting node_modules and running a fresh pnpm install; plain pnpm install may report "Already up to date" without repairing broken links.