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President Vladimir V. Putin of Russia last week. Russia’s reported deployment of a new type of missile presents another challenge to its relations with the United States. POOL PHOTO BY ALEXANDER ZEMLIANICHENKO By MICHAEL R. GORDON WASHINGTON —  Russia  has secretly deployed a new cruise missile despite complaints from American officials that it violates a landmark arms control treaty that helped seal the end of the Cold War, administration officials say. The move presents a major challenge for President Trump, who has vowed to improve relations with President Vladimir V. Putin of Russia and to pursue future arms accords. The new Russian missile deployment also comes as the Trump administration is struggling to fill key policy positions at the State Department and the Pentagon — and to settle on a permanent replacement for  Michael T. Flynn, the  national security adviser  who resigned  late Monday. Mr. Flynn stepped down after it was revealed that he had misled the vice president