Instead of editing the deep project file manually the settings can be altered by choosing Project → Properties. Alternatively you can press the right mouse button on the project name in the package explorer:
Refactoring is a very powerful tool in the eclipse framework. You can rename a deep project by choosing a project in the package explorer and pressing Shift+Alt+R. The project together with its associated deep project file will be renamed.
Make sure that your project name does not include dashes, spaces and umlauts.