AD-1103: Integrate patch apply with workflow persistence

[alph-cmky]

Summary

• Apply approved workflow patch proposals through the workflow registry when one is configured.
• Reject stale patch applications when the persisted workflow version differs from the proposal base version.
• Audit approved patch applications and stale rejected apply attempts.
• Preserve the existing preview-only behavior when no workflow registry is injected.
• Update the AD-1103 backlog checklist.

Testing

• TDD red check: pnpm test apps/server/src/patches/patch-service.test.ts failed because apply returned preview-only output and did not persist or reject stale versions.
• pnpm test apps/server/src/patches/patch-service.test.ts
• pnpm lint && pnpm format && pnpm typecheck && pnpm test && pnpm build

Stacked on #52.