A quote from the press release, on how this was done:
"When the photon exits the medium, its identity is preserved," Lukin said. "It's the same effect we see with refraction of light in a water glass. The light enters the water, it hands off part of its energy to the medium, and inside it exists as light and matter coupled together, but when it exits, it's still light. The process that takes place is the same it's just a bit more extreme – the light is slowed considerably, and a lot more energy is given away than during refraction."
The result of that process? As the photons exited the cloud, they were clumped together. That's a result of the nearby atoms; when one atom is excited, nearby atoms cannot be excited to the same degree, in an effect called a Rydberg blockade. So when a photon comes in, it excites nearby atoms, but when the next photon enters the cloud, it would excite nearby atoms to the same degree--which it can't do. So the first photon has to move out of the way. That's an interaction between photons, sort of, but with atoms as a mediator. What it means is that the two photons end up pushing and pulling each other through the cloud of atoms, and when they exit the cloud, they're clumped like a molecule, thanks to that continued interaction.
The scientists think this breakthrough could lead to improvements in quantum computing; photons are an excellent carrier for quantum information, but the lack of interaction between photons has limited the amount of information that can be carried. The paper appears in the journal Nature.