Ideally, both the configuration management repository and file system mirror the structure of the project in IBM® Rational® Rhapsody®. The following figure shows a Rational Rhapsody design, file structure, and configuration management repository synchronized with each other.

In some cases, changes you make to your model result in changes to the directories and files stored on the file system. Some examples include creating new units, renaming units, and moving units to new locations. Rational Rhapsody can update some of these changes in the configuration management system automatically, completing the three‑way synchronization without any additional steps. Use the configuration management tool to manually make the changes that cannot be accomplished using the configuration management tool from within Rational Rhapsody.
In other cases, it is easier to make changes to the structure of your project outside of Rational Rhapsody, particularly when moving files from a flat structure to a hierarchical structure. You can make these changes to your file system and your configuration management system directly. When you next open Rational Rhapsody, you are asked to locate the missing units. The product prompts you with two options for restoring synchronization: