The menu bar option File entry has been replaced by a new menu contribution to be able to control the actions that should be enabled or disabled based on the selected resource and to also be able to replace the default wizards available for those actions. New wizards have been defined using the org.eclipse.ui.newWizards extension point and new commands have also been defined as menu contributions with filtering conditions:

The commands can be either existing commands, as the Close command (org.eclipse.ui.file.close) or new commands, as the Move Resource command

In order to remove a menu bar contribution and replace it with your own, the hideMenuItem perspective property as part of a perspective extension (org.eclipse.ui.perspectiveExtensions extension point) is used and can be also used for any further configuration of the menu bar: