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.
