DORAL, Fla. — The military commander who initially oversaw the Pentagon’s attacks on boats in the Caribbean Sea and the eastern Pacific retired Friday, leaving several issues about the strikes unanswered.

The officer, Adm. Alvin Holsey, abruptly announced in October that he would step down at the end of the year from his job as the head of U.S. Southern Command, which oversees all operations in Central and South America.

The Trump administration has said that boats in the region were smuggling drugs and criminals into the United States, and the Pentagon rapidly built up some 15,000 forces there in what it called a major counterdrug and counterterrorism mission.

It was still not entirely clear why Holsey was departing a year into what is typically a three-year job and in the midst of the

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