Without pnpm-workspace.yaml, pnpm install --frozen-lockfile can't discover
the apps/api workspace member, causing "Already up to date" and tsc not found.
Also removes stale packages/* entry from pnpm-workspace.yaml (no packages/
directory exists in the dev branch).
Fixes: GRO-1231
Co-Authored-By: Paperclip <noreply@paperclip.ing>