Merge class config dicts when flattening flags

Closes ipython/ipython#10088

This is not a technically correct fix, but it's probably good enough for
any cases in our code. The whole flatten_flags method seems like a very
awkward workaround to make one priority ordering more important than
another. It only 'flattens' one level of inheritance, and it ignores
that parent classes may be instantiated. It skips over any parent class
with multiple configurable children.

traitlets/config/application.py

@@ -522,7 +522,12 @@ def flatten_flags(self):
                 # exactly one descendent, promote flag section
                 if len(children) == 1:
                     cls = children[0]
-                newflag[cls] = subdict
+
+                if cls in newflag:
+                    newflag[cls].update(subdict)
+                else:
+                    newflag[cls] = subdict
+
             if not isinstance(key, tuple):
                 key = (key, )
             for k in key: