The most common and most likely answer to this crossword clue is the 13 letter word STATIONMASTER
I've seen this crossword clue in The Daily Telegraph
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More clues leading to the result STATIONMASTER
Buddy explains!
The straight part
We know that "Man in command at Waterloo" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case man in command at waterloo = stationmaster.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does STATIONMASTER mean?
STATIONMASTER noun- The person in charge of a railroad station, usually an employee of a particular railroad by which the station is owned, but sometimes an employee of a separate corporation, such as one owning a station used by two or more railroads.