You can reorganize proxies in the Requirement Explorer view so they match the domain element structure in specific views such as the Navigator. You need to reorganize proxies if you move domain elements around and want to keep your proxies in locations meaningful to your project.
To reorganize requirement proxies, in the Requirements Explorer view, right-click the Eclipse Element Proxies folder; and then click Organize Proxies.
The Eclipse Element Proxies folder synchronizes with the appropriate view; all empty packages are deleted from the Requirement Explorer view.