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(Please let me know if the title could be improved)
I have a class C defined in submodule B of module A, so full python name would be A.B.C. But the class is imported in the __init__.py of A, thus exposed from the module A. And it is imported from there by other packages.
Autoapi does only resolve the name to A.C, this causes that cross-reference from other packages don't work. As in the objects.invA.C is not available, only A.B.C.