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.

resources/Project Templates/Basic/Boot.js

@@ -1,4 +1,4 @@
-BasicGame = {};
+var BasicGame = {};
 
 BasicGame.Boot = function (game) {
 
@@ -17,33 +17,33 @@ BasicGame.Boot.prototype = {
     create: function () {
 
         //  Unless you specifically know your game needs to support multi-touch I would recommend setting this to 1
-        this.game.input.maxPointers = 1;
+        this.input.maxPointers = 1;
 
         //  Phaser will automatically pause if the browser tab the game is in loses focus. You can disable that here:
-        this.game.stage.disableVisibilityChange = true;
+        this.stage.disableVisibilityChange = true;
 
         if (this.game.device.desktop)
         {
             //  If you have any desktop specific settings, they can go in here
-            this.game.stage.scale.pageAlignHorizontally = true;
+            this.scale.pageAlignHorizontally = true;
         }
         else
         {
             //  Same goes for mobile settings.
             //  In this case we're saying "scale the game, no lower than 480x260 and no higher than 1024x768"
-            this.game.stage.scaleMode = Phaser.StageScaleMode.SHOW_ALL;
-            this.game.stage.scale.minWidth = 480;
-            this.game.stage.scale.minHeight = 260;
-            this.game.stage.scale.maxWidth = 1024;
-            this.game.stage.scale.maxHeight = 768;
-            this.game.stage.scale.forceLandscape = true;
-            this.game.stage.scale.pageAlignHorizontally = true;
-            this.game.stage.scale.setScreenSize(true);
+            this.scale.scaleMode = Phaser.ScaleManager.SHOW_ALL;
+            this.scale.minWidth = 480;
+            this.scale.minHeight = 260;
+            this.scale.maxWidth = 1024;
+            this.scale.maxHeight = 768;
+            this.scale.forceLandscape = true;
+            this.scale.pageAlignHorizontally = true;
+            this.scale.setScreenSize(true);
         }
 
         //  By this point the preloader assets have loaded to the cache, we've set the game settings
         //  So now let's start the real preloader going
-        this.game.state.start('Preloader');
+        this.state.start('Preloader');
 
     }
 

resources/Project Templates/Basic/Game.js

@@ -13,7 +13,8 @@ BasicGame.Game = function (game) {
     this.sound;		//	the sound manager - add a sound, play one, set-up markers, etc
     this.stage;		//	the game stage
     this.time;		//	the clock
-    this.tweens;	//	the tween manager
+    this.tweens;    //  the tween manager
+    this.state;	    //	the state manager
     this.world;		//	the game world
     this.particles;	//	the particle manager
     this.physics;	//	the physics manager
@@ -44,7 +45,7 @@ BasicGame.Game.prototype = {
 		//	Stop music, delete sprites, purge caches, free resources, all that good stuff.
 
 		//	Then let's go back to the main menu.
-		this.game.state.start('MainMenu');
+		this.state.start('MainMenu');
 
 	}
 

resources/Project Templates/Basic/MainMenu.js

@@ -35,7 +35,7 @@ BasicGame.MainMenu.prototype = {
 		this.music.stop();
 
 		//	And start the actual game
-		this.game.state.start('Game');
+		this.state.start('Game');
 
 	}
 

resources/Project Templates/Basic/Preloader.js

@@ -53,7 +53,7 @@ BasicGame.Preloader.prototype = {
 		if (this.cache.isSoundDecoded('titleMusic') && this.ready == false)
 		{
 			this.ready = true;
-			this.game.state.start('MainMenu');
+			this.state.start('MainMenu');
 		}
 
 	}