Fix MCP tool allowlist filtering in SDK run path #6075

Job	Run time
build-and-check	3m 2s
test-integration-packages/internal	1m 14s
test-integration-packages/billing	1m 0s
test-integration-web	43s
test-integration-packages/agent-runtime	39s
test-integration-cli	50s
test-integration-common	42s
test-integration-sdk	1m 16s
test-cli	48s
test-packages/billing	43s
test-common	42s
test-packages/agent-runtime	52s
test-packages/internal	52s
test-web	48s
test-sdk	49s
test-.agents	58s
	15m 58s

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