Verify latest release

• I verified that the issue exists in the latest pnpm release

pnpm version

11.0.0-rc.5

Which area(s) of pnpm are affected? (leave empty if unsure)

No response

Link to the code that reproduces this issue or a replay of the bug

No response

Reproduction steps

pnpm init
pnpm add cowsay
pnpm ci

Describe the Bug

This leaves a node_modules dir with only a .pnpm-workspace-state-v1.json file.

A subsequent pnpm install just reports "Already up to date", and doesn't install anything.

The same is the case if you run pnpm clean and pnpm install separately.

Expected Behavior

pnpm ci should install node_modules
pnpm clean should delete .pnpm-workspace-state-v1.json

Which Node.js version are you using?

22.18.0

Which operating systems have you used?

• macOS
• Windows
• Linux

If your OS is a Linux based, which one it is? (Include the version if relevant)

No response