Fix stdin stream queued messages and command output streaming

[cte]

Summary

• ensure queued stdin-stream messages are preserved and drained correctly during long-running command execution
• stream command execution output chunks as they are produced in stream-json mode
• keep command-output events correlated to the originating command execution in emitted JSON events
• add/adjust tests covering queued message drain and command output streaming behavior

Validation

• lint and typecheck passed via pre-commit/pre-push hooks during commit/push

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