[Bug] deprecated package create unnecessary git diff in lock file

[Airkro]

Verify latest release

• [x] I verified that the issue exists in the latest pnpm release

pnpm version

10.8.0

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

Lockfile

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

No response

Reproduction steps

Install some deprecated packages in the project.

Run: pnpm install / pnpm update / pnpm dedupe

Describe the Bug

If some deprecated packages are installed:

Running pnpm update will add deprecated messages in the lock file if they are missing. Running pnpm dedupe will remove some deprecated messages in the lock file for unknown reasons. Running pnpm install will not change the lock file, even though deprecated messages are missing.

The differences in these behaviors have led to useless git diffs, causing unnecessary burdens on the review process.

Expected Behavior

Treat deprecated message the same way, when install, dedupe, or update.

Which Node.js version are you using?

22.10.0

Which operating systems have you used?

• [ ] macOS
• [x] Windows
• [ ] Linux

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

No response

[maclockard]

Just noting this also potentially breaks git hooks / CI checks that dedupe was properly run since it will result in a diff when the deprecated notice is erroneously removed!