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Managing configuration changes, or overrides to Open Atrium's default Features, is done using 'Features Override'. A description of what Features Override is, why we need to use it, and how to capture overrides can be found here: https://www.drupal.org/node/1313910
A blog post about Features Overrides, by the OA project lead, can be found here:
http://www.phase2technology.com/blog/how-to-override-features
(Discussion about improving this page can be found here: https://drupal.org/node/2199519)