What version of Turborepo are you using?

1.6.3

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

pnpm

What operating system are you using?

Linux

Describe the Bug

When running turbo prune, pnpm.patchedDependencies is set to {} in the out directory.

Expected Behavior

patchedDependencies should stay as they were before running tubro prune, or an option to keep some / all patched dependencies should be added.

To Reproduce

1. Create a turborepo with a package and install a dependency to it
2. Patch the dependency using pnpm patch and pnpm commit-patch
3. Run turbo prune --scope=package and observe out/package.json

In the reproduction repo I've already done this, so both the input and output can be seen in the repo.

Reproduction Repo

https://github.com/marekvospel/turborepo-prune-removes-patched