Uniformize layer names, script methods and documentation

- Back to 1-based layer names to make it clearer in editor UI
- Layer bit accessors are renamed to layer value and 1-based too
- Uniform errors and documentation in render and physics
- Fix a few remaining collision_layer used in place of collision_mask

doc/classes/PhysicsShapeQueryParameters3D.xml

@@ -18,7 +18,7 @@
 			If [code]true[/code], the query will take [PhysicsBody3D]s into account.
 		</member>
 		<member name="collision_mask" type="int" setter="set_collision_mask" getter="get_collision_mask" default="2147483647">
-			The physics layer(s) the query will take into account (as a bitmask). See [url=https://docs.godotengine.org/en/latest/tutorials/physics/physics_introduction.html#collision-layers-and-masks]Collision layers and masks[/url] in the documentation for more information.
+			The physics layers the query will detect (as a bitmask). By default, all collision layers are detected. See [url=https://docs.godotengine.org/en/latest/tutorials/physics/physics_introduction.html#collision-layers-and-masks]Collision layers and masks[/url] in the documentation for more information.
 		</member>
 		<member name="exclude" type="Array" setter="set_exclude" getter="get_exclude" default="[]">
 			The list of objects or object [RID]s that will be excluded from collisions.