Add ability to remove menus

Closes #3216
Will using `indexOf` work here since `item` is an `Object` and that will use `===` equality which will require you to call `remove` with the exact same object that you called `add`.

So for example this would fail to remove the `Test` menu:

```coffee
atom.menu.add(label: Test)
atom.menu.remove(label: Test) # Test would still be there since it is a different object.
```