cli: Better handle thinking blocks from native model reasoning #5551

Job	Run time
build-and-check	2m 30s
test-integration-packages/billing	1m 8s
test-integration-packages/internal	1m 1s
test-integration-sdk	40s
test-integration-common	43s
test-integration-web	39s
test-integration-cli	42s
test-packages/billing	45s
test-integration-packages/agent-runtime	43s
test-packages/agent-runtime	57s
test-web	49s
test-packages/internal	52s
test-cli	1m 16s
test-common	41s
test-.agents	47s
test-sdk	42s
	14m 55s

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