Symbolism, Imagery, Allegory
Every buddy cop movie needs an older chief with a chewed-up cigar permanently hanging out of his mouth—it's a symbol of age, power, and most of all authority. So what if Artemis Fowl isn't a buddy cop movie, and the older chief also happens to be a fairy? Root already has everything else—the flabby body of a former officer now working at a desk, the tendency to frighten new recruits, the traditional dislike of fancy "gadgetry" (kids these days).
What really makes Root the boss, however, is the constant cloud of unpleasant cigar smoke that surrounds him, making his presence the most obvious one in the room. When you smell those reeking fumes, you know Root is in charge:
Commander Root was sucking on a particularly noxious fungus cigar. Several of the Retrieval Squad had nearly passed out in the shuttle. [...] Of course, no one said anything [...].(5.1)
The number one sign someone's totally running the show is that they do something that seriously bugs the people around them but no one dares voice complaint. And pretty much every time Root's around, his cigar makes sure there's no confusion about who's in charge.