storage: migrate core execution state to SQLite

[likun666661]

Summary

Implements Stage 3 of #1649 after #1677.

• make runtime.sqlite canonical for AgentRun headers/events/projections, root-turn admissions/proofs, interactions, message receipts/Host epochs, and ShellRun metadata
• import legacy JSON/JSONL state once through per-store cutover journal entries, with logical fingerprints, atomic copy+validation, crash failpoints, restart resume, and fail-closed source drift detection
• wire CLI, Desktop/Runtime Host, and Headless execution facades to the shared SQLite repositories and close their database leases with the existing persistence lifecycle
• preserve recovery/evidence semantics, including ENOENT behavior and event_corrupt projection for damaged AgentRun evidence
• keep transcript JSONL and payload/artifact files unchanged; task ledger, plan, deep research, pricing, and artifact metadata remain Stage 4

Planning: #1649 (comment)

Verification

• npm --workspace @maka/storage run test — 836 passed, 0 failed, 1 skipped
• npm --workspace @maka/runtime-host run test — passed
• npm --workspace maka-agent run test — passed
• npm --workspace @maka/headless run test:dist — passed
• storage, Runtime Host, Headless, and CLI typechecks passed
• Biome and git diff --check passed