Through the night that covers you, - Appearance ref; "Ebony satin pelt with a glossy sheen."
hushed as all of heart may be, - Personality/Name ref; Caleb's voice is described to be "a mere whisper on the wind, words spoken in a hushed tone, a husky whisper" and in his profile it's stated that he "only completely opens up to few" which can also be a reference to his heart being 'hushed'. Caleb also means All of and Heart.
parts of you tell a different story entirely. - History/personality ref; He is described to have impeccable manners, but his body is covered in scars.
Little spy, can you catch me? - Little is a reference to him being very young. When you search for Caleb the first page that comes up is this one: http://en.wikipedia.org/wiki/Caleb and it explains that Caleb was one of the twelve spies sent by Moses into Canaan, hence spy.