As default Project Layout in Project Explorer has been switched to hierarchical, a new preference is available for RCP providers who want to force Flat layout by default instead. The preference is
org.eclipse.ui.navigator.resources/defaultToFlatLayout and can be set to
plugin_customization.ini or programatically before Project Explorer opens
for the first time, in order to force a Flat project layout. Subsequent change to this preference after first initialization of Project Explorer will have no effect.