Autosummary generates incorrect stub files for nested classes (openff-toolkit)

Describe the bug
With autosummary_generate = True in conf.py and a class implemented within another class, stubs for the inner class are written as though the outer class is a module, leading to autodoc warnings.

To Reproduce
Steps to reproduce the behavior:

$ git clone https://github.com/openforcefield/openff-toolkit
$ cd openff-toolkit
$ git checkout fewer-docs-warnings
$ conda env create -f=docs/environment.yml -n openfftkdev
$ conda activate openfftkdev
$ pip install -e .
$ cd docs
$ make html

Alternatively, create a class within a class:

class Outer:
    """Wonderful docstring for an outer class"""
    class Bar:
        """Another docstring"""
        pass

and attempt to document it with autodoc and autosummary with autosummary_generate = True in conf.py

Expected behavior
The project should compile without autodoc: failed to import class warnings.

Your project
https://github.com/openforcefield/openff-toolkit

Environment info

• OS: Manjaro Linux
• Python version: 3.7.9
• Sphinx version: 3.4.3
• Sphinx extensions: sphinx.ext.autodoc, numpydoc, sphinx.ext.autosummary, sphinx.ext.doctest, sphinx.ext.todo, sphinx.ext.mathjax, sphinx.ext.viewcode, sphinx.ext.intersphinx, nbsphinx, m2r2
• Extra tools: Conda 4.9.2 for package and environment management

Additional context

The documentation compiles with warnings:

WARNING: autodoc: failed to import class 'AngleType' from module 'AngleHandler'; the following exception was raised:
No module named 'AngleHandler'
WARNING: autodoc: failed to import class 'BondType' from module 'BondHandler'; the following exception was raised:
No module named 'BondHandler'
WARNING: autodoc: failed to import class 'GBSAType' from module 'GBSAHandler'; the following exception was raised:
No module named 'GBSAHandler'
WARNING: autodoc: failed to import class 'ImproperTorsionType' from module 'ImproperTorsionHandler'; the following exception was raised:
No module named 'ImproperTorsionHandler'
WARNING: autodoc: failed to import class 'LibraryChargeType' from module 'LibraryChargeHandler'; the following exception was raised:
No module named 'LibraryChargeHandler'
WARNING: autodoc: failed to import class 'ProperTorsionType' from module 'ProperTorsionHandler'; the following exception was raised:
No module named 'ProperTorsionHandler'
WARNING: autodoc: failed to import class 'vdWType' from module 'vdWHandler'; the following exception was raised:
No module named 'vdWHandler'

These warnings are produced by the auto-generated stub files:

• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.AngleType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.BondHandler.BondType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType.rst
• docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler.vdWType.rst

The following patch (with autosummary_generate_overwrite = False added to docs/conf.py) resolves the issue for the GBSAHandler instance:

--- a/docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType.rst
+++ b/docs/api/generated/openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType.rst
@@ -3,10 +3,10 @@
 
 .. currentmodule:: openff.toolkit.typing.engines.smirnoff.parameters
 
-.. autoclass:: GBSAHandler.GBSAType
+.. autoclass:: openff.toolkit.typing.engines.smirnoff.parameters::GBSAHandler.GBSAType
 
    
-   .. automethod:: __init__
+   .. automethod:: openff.toolkit.typing.engines.smirnoff.parameters::GBSAHandler.GBSAType.__init__
 
    
    .. rubric:: Methods

This patch is based on advice from Stack Overflow. Obviously manually editing auto-generated files is not an acceptable solution.

I'd be happy to submit a PR if a maintainer could suggest their preferred way of fixing this :)

Start with docs/conf.py and the generated stubs under docs/api/generated/, then reproduce the warnings with make html using the documented environment. Trace how autosummary handles nested classes such as GBSAHandler.GBSAType; done means generated stubs use importable references and the documentation builds without autodoc import warnings.