fix(data): recalibrate checkpoint counters

[shifang0511]

Summary

• Add CheckpointManager.recalibrate() to sync drift-prone L0/L1 counters with live store counts, falling back to JSONL line counts when no store is available.
• Recalibrate during core startup before scheduler restore and after memory-cleaner cleanup.
• Add regression coverage for JSONL fallback, store-preferred counts, and cleaner-triggered recalibration.

Test Plan

• npm test
• npm run build
• git diff --check

Fixes #157