Fix MCP tool allowlist filtering in SDK run path (#501) #6079

Job	Run time
build-and-check	2m 52s
test-integration-packages/billing	1m 11s
test-integration-packages/internal	1m 19s
test-integration-common	38s
test-integration-packages/agent-runtime	42s
test-integration-cli	52s
test-integration-sdk	1m 19s
test-integration-web	47s
test-packages/internal	54s
test-packages/billing	45s
test-packages/agent-runtime	1m 2s
test-cli	1m 18s
test-.agents	40s
test-common	45s
test-sdk	43s
test-web	51s
	16m 38s

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