Move pnpm config into pnpm-workspace.yaml

[crusty-voidzero]

Context

While landing PR #1222 (#1222), @cpojer noted in #1222 (comment) that our pnpm configuration should live inside pnpm-workspace.yaml. Right now pieces of the configuration are spread across .npmrc, package.json, and local developer notes, which makes it harder to understand/override defaults.

Tasks

• Inventory every place we set pnpm options today (.npmrc, package.json scripts, docs, CI bootstrap scripts).
• Move the shared settings into pnpm-workspace.yaml using pnpm's documented schema (packages, packageExtensions, neverBuiltDependencies, overrides, etc.).
• Remove or simplify redundant config files once the workspace file is the source of truth.
• Update docs/onboarding scripts to mention the new single configuration location and confirm CI still picks it up.