fix(sync): preserve partial scan history

[xingkaixin]

Summary

• propagate snapshot completeness and explicit removals from scan workers to persistence
• preserve durable session facts when a windowed or degraded scan publishes a partial snapshot
• keep confirmed source deletions effective without treating omitted history as deleted

Root cause

The refresh pipeline discarded the scan scope/completeness before it reached cache and search-index persistence. A partial publication was therefore interpreted as a complete replacement, which could delete sessions, messages, file activity, and indexed content outside the scan window.

Validation

• pnpm lint
• pnpm format:check
• pnpm build
• pnpm test
• pnpm test:e2e

Closes CS-175.