refactor(monorepo): add workspace foundation

[geminixiang]

Summary

• add npm workspace foundation with chat, agent-runtime, and mikan packages
• move the existing app into packages/mikan while preserving the @geminixiang/mikan CLI package
• centralize conversation log.jsonl write helpers in @geminixiang/mikan-chat
• document the chat log / agent runtime boundary ADR
• update workflows, tsconfig, vitest, and knip for workspace paths

Verification

• npm run build
• npm test
• npm run knip
• npm run lint (0 errors; existing no-await-in-loop warnings remain)
• npm pack --workspace @geminixiang/mikan --dry-run
• Slack E2E: https://github.com/geminixiang/mikan/actions/runs/27193829231

[geminixiang]

Closing because this item has had no activity for more than 30 days. Please reopen it or create a fresh follow-up if the work is still relevant.