Fix Issue #1273

Added Lua index registry clear routine to `destroy` method of classes that use it.
If this is left to GC, the abandoned userdata would stay in memory for one full extra cycle.

Prettified the code slightly. Clarified some comments. Refactored `Fixture` class `udata` name.
Removed Reference class include from `Shape` (it doesn't use it).

src/modules/physics/box2d/Body.h

@@ -69,7 +69,7 @@ public:
 	friend class Shape;
 	friend class Fixture;
 
-	// The Box2D body. (Should not be public?)
+	// Public because joints et al ask for b2body
 	b2Body *body;
 
 	/**