InputManager extends Controls which is a deprecated class.
When one uses the addMapping method from the InputManager, the actual implementation appears in the Controls. So eclipse thinks (and rightfully so) you're using a mehtod from a deprecated class, which is why he gives you deprecation warnings.
I suggest that either we'll avoid using the Controls class altogether, or, we'll deprecated not the class itself, but all the methods in the class (or maybe the actual constructor. Deprecating the constructor makes sure we won't use the class, wouldn't it).
Should I open a bug for that?
No, at this point no-one should be using the class anymore. So we can safely just get rid of the Controls class.
Porting code over from a jME2 project into JME3 I saw these deprecation warnings going on with inputManager while using addmapping and addlistener. Is it going under another overhaul anytime soon? Because I think the latest version works swimmingly from what I can tell so far 
The InputManager system is complete at this stage. I was actually talking about the Controls class, what I am going to is simply merge the Controls class into the InputManager, thus removing the deprecation warnings.
Speaking about input system, it would be great to add method to change mouse location. Actually I did it in my local copy, by extending MouseInput interface and all implementing it for all its children:
public interface MouseInput extends Input {
...
public void setMouseLocation(int x, int y);
}
public class LwjglMouseInput implements MouseInput {
...
public void setMouseLocation(int x, int y) {
Mouse.setCursorPosition(x, y);
}
}
Should it be permanent change or you have another ideas?
The Controls and InputManager classes have been merged, and the old binding methods were removed.
KevinK: Why do you need to change the mouse location?
For example to set cursor to center of the screen when user switches to menu from game.