I have a package:
foo.py has a class Foo. In __init__.py I import class Foo
The value of the __module__ attribute is the name of the module in which a class/function/method was defined (see https://docs.python.org/2.7/reference/datamodel.html). The attribute is writable so it can be redefined in __init__.py:
Foo.__module__ = "foo"
Now if you use .. automodule:: foo, the qualified name of the Foo class will be shown as foo.Foo in the generated module documentation.
As an alternative to __module__-fiddling, you can use autoclass instead of automodule.
.. autoclass:: foo.Foo will produce the wanted output.