__all__ not respected when going from 3.0.0 to 3.1.0

[dstansby]

Over at zarr we've noticed that bumping autoapi from 3.0.0 to 3.1.0 results in __all__ not being respected by autoapi for some sub-modules. The same issue still persists with the latest version, 3.3.1.

An example failing build can be found at https://readthedocs.org/projects/zarr/builds/25599267/.

Sorry that's not much to go on, but I'm hoping I can bisect to work out which commit caused the issue next.