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Repro:
This is because we obtain the list of dependencies using config.lockfileFolder in makeEnv, but since the dependencies are located inside their own folders (in the unplugged directory) Yarn doesn't see the real project as being the lockfileFolder - so it cannot find the .pnp.js file.
Cf:
/private/tmp/canvas/.pnp/unplugged/npm-canvas-2.1.0-9abbfee6051b16666332ad0a8a2fd142e29039a1/node_modules/canvas/.pnp.js