perf(agent-runtime): skip thinking token progress persistence

[jerryliang64]

Summary

• exclude system/thinking_tokens progress counters from thread message persistence
• keep those events available through /runs/stream and run-event replay
• preserve the final assistant message, including its complete thinking content
• cover the behavior at both MessageConverter and AgentRuntime integration levels

Root cause

After a run commits, the incremental message flusher attempts to mirror every executor message into the thread store. thinking_tokens is emitted frequently as a progress counter, so persisting it creates one awaited remote append per update on OSS/FUSE-backed stores and backpressures consumption of subsequent model events.

The counter is transient metadata rather than conversation history. Filtering it at the existing storage boundary removes that write amplification without changing the streaming protocol or final transcript.

Validation

• core/agent-runtime: ut run test (210 passing)
• core/agent-runtime: ut run tsc
• core/agent-runtime: ut run tsc:pub
• repository lint: ut run lint
• independent correctness/security review: LGTM

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