fix(daemon): stabilize checkout pr cache keys

[ovdmar]

Summary

• Stabilize checkout PR cache keys so PR cards remain visible after PR binding updates bump workspace_checkouts.updated_at.
• Stop structured root workspaces from spending GitHub VC/CI refreshes while still refreshing checkout children.
• Enter GitHub cooldown at 99% used for core/graphql quota, before the remaining quota reaches zero.

Plan

Inline / trivial

Test plan

• pnpm vitest run apps/daemon/src/workspaces-pr-state-route.test.ts apps/daemon/src/provider-refresh-job.test.ts apps/daemon/src/github-provider-state.test.ts apps/daemon/src/checkout-pr-primer.test.ts apps/daemon/src/app-github-quota.test.ts
• pnpm lint
• pnpm typecheck
• pnpm check:size
• make check passes locally
• Manual QA per the How-to-QA section below

How to QA

1. Pull the branch: git checkout fb-checkout-pr-cache-key
2. Install: pnpm install
3. Full check: make check
4. Start the daemon + web in dev mode: pnpm dev
   • Daemon: http://localhost:4010
   • Web cockpit: http://localhost:5173

• Open the cockpit stats right panel for a structured workspace checkout that has an associated PR, and verify the PR card is visible.
• Trigger or wait for a checkout PR binding refresh, then refresh /api/workspaces/pr-state and verify the same checkout PR summary is still present.
• Exercise /api/integrations/github/quota with a near-exhausted core/graphql quota and verify provider polling enters cooldown before quota reaches zero.