Fixed some inconsistencies and oddities in physics-handling code

I'm not sure if this fixes or breaks anything, but it's worth a shot.

Barotrauma/BarotraumaShared/Source/Map/Structure.cs

@@ -835,6 +835,7 @@ namespace Barotrauma
             {
                 StairDirection = StairDirection == Direction.Left ? Direction.Right : Direction.Left;
                 bodies.ForEach(b => GameMain.World.RemoveBody(b));
+                bodies.Clear();
 
                 CreateStairBodies();
             }

Barotrauma/BarotraumaShared/Source/Map/Submarine.cs

@@ -1208,9 +1208,9 @@ namespace Barotrauma
                 Item.ItemList.Clear();
             }
 
-            PhysicsBody.RemoveAll();
+            Ragdoll.RemoveAll();
 
-            Ragdoll.list.Clear();
+            PhysicsBody.RemoveAll();
 
             GameMain.World.Clear();