Why could this sentence not be "It speaks clearly,"? There are no obvious gender identifiers and "it" is the best way to communicate gender neutrality in English.
My guess is usually only people "speak" and people are not referred to as "it". Ah a better answer it is an order. You use the imperative. "Habla" is the imperative for "tú"/"you". "Habla claramente" = "You speak clearly" or since "you" can be implied simply "speak clearly". http://www.spanishdict.com/conjugate/hablar
It is a command, but at this point I am studying adverbs. Commands are further down the tree, for me. I got it correct with "He speaks clearly" "Habla is also 3rd person singular, as you probably know that already.