Fix source selection, archive idempotency, and Gemini tool metadata

[suguanYang]

Summary

• keep explicit stale or pending source selections from falling back to unrelated ready documents
• treat Knowhere document-not-found archive responses as idempotent so local source deletion can complete
• strip provider metadata from tool-result continuation messages while preserving assistant tool-call metadata for Gemini thought signatures

Tests

• pnpm exec vitest run src/components/workspace-source-state.test.ts src/domains/sources/route-service.test.ts src/agent-harness/runtime.test.ts
• pnpm exec vitest run src/components/workspace-source-workflow.test.ts src/components/workspace-selected-chunks.test.ts src/components/workspace-shell.test.ts src/domains/chat/index.test.ts
• pnpm lint
• pnpm run typecheck

Note: typecheck passes and prints the existing Effect diagnostic in src/domains/sources/counts.ts about Effect.void.

[vercel]

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Project	Deployment	Actions	Updated (UTC)
knowhere-notebook-staging	Ready	Preview, Comment	Jul 5, 2026 3:53pm

1 Skipped Deployment

Project	Deployment	Actions	Updated (UTC)
knowhere-notebook	Ignored		Jul 5, 2026 3:53pm