Phaser.StageScaleMode has been renamed to ScaleManager and moved from the system folder to the core folder. It's still available under game.scale.
If your game references the old Phaser.StageScaleMode consts like SHOW_ALL you need to update them to Phaser.ScaleManager, i.e. Phaser.ScaleManager.SHOW_ALL.
All of the Project Templates have been updated to reflect the above change.