There are two ways to change contexts. The new awesomeness is to use Features or other exportable techniques to create a new version of your modified contexts, and push the old ones out of the way.
However, when I avoid hacking [atrium] core, I prefer the old way–today that’s alter hooks.
Bio in Brief: I spend a lot of time thinking about how to build collaboration tools in Drupal. Before that I noodled about with Java looking at long-term data preservation and geospatial data discovery.