Verify latest release

I verified that the issue exists in the latest pnpm release

pnpm version

8.14.1

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

https://github.com/RuudBurger/pnpm-patch-problem

Reproduction steps

1. Git clone the repo
2. Run pnpm install
3. packages/package1 has the patch applied, packages/package2 doesn't
4. Run pnpm dlx del-cli "**/node_modules"; pnpm i
5. Both package1 and package2 have the patch applied
6. Run pnpm dlx del-cli "**/node_modules"; pnpm store prune; pnpm i
7. Same as step 3.

Extra:

1. Delete only the package2 node_modules with rm -Rf packages/package2/node_modules; pnpm i
2. package1 has the patch applied twice
3. Do this multiple times and you end up with
   
4. The package2 has the patched applied also, minus 1. So it uses the already patched package as a basis, and re-applies the patch after it copies it.

Describe the Bug

See above. The setting node-linker=hoisted is key here. Our repo used react-native and it doesn't work well without the hoisted method.

Expected Behavior

Patching file should be consistent, but after store prune it patches the filed differently.

This means that a CI with no cache, behaves differently then a local dev environment that never did a pnpm store prune.

Which Node.js version are you using?

18.18.2

Which operating systems have you used?

macOS

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

No response