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The `--prefix` option (renamed to `dir`) was applied to options after `getWorkspaceDir` had already run, so workspace detection fell back to `process.cwd()` and missed the manifest at the prefix dir. As a result, running pnpm from outside the project (e.g. `pnpm --prefix=child install` from the parent dir) silently skipped settings declared in `child/pnpm-workspace.yaml`. Backport of #11549 to release/10. Closes #11535.