How Agents Of S.h.i.e.l.d Got Good (spoilers Inside)

Spoiler: Secret Warriors

Caterpillar was the name of the program that gave birth to Secret Warriors which is a small team lead by Daisy Johnson (Skye). She has a group of super powered people that was instrumental in the larger Secret Invasion story-line. It was a measure started by Nick Fury where he has a bunch of small teams he's kept secret from everyone including each other.

In the show they use it for what I assume is just a nice easter egg for the fans. It does imply though that Skye will get her own team over super-powered peeps to run secret missions.