In your root pnpm-workspace.yaml, make sure it includes all packages:

packages:
  - "apps/*"
  - "packages/*"

Then hoist shared deps to the root by adding them at the top-level package.json:

{
  "dependencies": {
    "zod": "^3.24.2",
    "sonner": "^2.0.6"
  }
}

Then run:
pnpm install