fix(runtime): prepare checkpoint directories before backup

[Yevanchen]

Summary

• materialize declared checkpoint directories before Cloudflare Sandbox backup
• allow stale/missing pet session workspaces to converge instead of leaving the subject permanently backing_up
• assert every checkpoint target is prepared in the recycle test

Production evidence

A pet subject repeatedly failed maintenance because an old session workspace no longer existed; the operation retried every ten minutes and blocked new runs.

Verification

• bun test apps/api/tests/runtime-subject-recycle.test.ts
• just tc-package @mosoo/api
• focused formatting checks
• git diff --check