The situation is explained by Saurik in a post on Cydia:
The key thing to realize is that Intelliborn, the company that brought you such products as IntelliScreen and MyWi, are the same developers who created Rock Your iPhone.
Unfortunately, due to some early miscommunication, rather than us being in a position where we were cooperating on platforms like Cydia, we ended up spending most of our time competing with each other over the course of the last two years.
This was not good: Rock ended up wasting a ton of effort implementing Cydia, while SaurikIT got dragged into an "apps battle" to compete with the Rock exclusives from Intelliborn.
The primary goal of this new world, then, is to put everyone "back on task", with a true collaboration rather than this incessant competition.
For users who were happy with Rock due to its speediness. Saurik says this was because of some incorrect/dangerous shortcuts which led to the "essential upgrade" that was required for Spirit and then crashed many devices. Now that the apps competition is over, Saurik will be able to concentrate on platform issues full time and hopefully improve performance.
As part of the collaboration, Rock's backup feature is being implemented in Cydia and all previous Rock backups and licenses will be merged into the Cydia database. Comments and ratings also being looked at and Saurik is consulting with the major repos on different implementation ideas.
This announcement should come as welcomed news to jailbreakers who will benefit from being able to get all their apps in one place as well as enjoy the improvements to Cydia.