Verify canary release

• I verified that the issue exists in the latest Turborepo canary release.

Link to code that reproduces this issue

https://github.com/gerbyzation/pnpm-v9-turbo-prune-injected-deps-repro

What package manager are you using / does the bug impact?

pnpm

What operating system are you using?

Mac

Which canary version will you have in your reproduction?

2.0.0-canary.0

Describe the Bug

When a workspace uses injected dependencies and the new pnpm lockfile format turbo prune will break with the following error:

❯ pnpm exec turbo prune --scope application
Generating pruned monorepo for application in /Users/gerbenneven/projects/pnpm-turbo-prune-repro/out
 - Added application
 - Added library
  × No lockfile entry found for 'link:../../../libraries/library'

Expected Behavior

turbo prune --scope application should create a directory with pruned repo

To Reproduce

Clone and follow steps in https://github.com/gerbyzation/pnpm-v9-turbo-prune-injected-deps-repro for repro

Additional context

No response