when generating the language runtime the previous manua configurations are lost

[dvojtise]

In GEMOc we use the org.eclipse.emf.ecoretools.registration.ui.ecoreAutoRegisterBuilder to automatically register the ecore in the current eclipse so ECL can work out of the box without having to deploye the plugin. This information is stored in the .project as a buildCommand. Unfortunatly, when generating the runtime for the language the .project file is completly overriden be a new one that doesn't contains this inforamtion anymore.