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Migrate to Pybind11 v3#30291

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PR summary

This was just released, so we probably don't want to make a hard cut-off here, but this is just a check to see how the new options work out without any attempt to maintain backwards-compatibility.

PR checklist

As ofpybind/pybind11#5212, pybind11 now uses`numpy.typing.NDArray` instead of `numpy.ndarray`, and as ofpybind/pybind11#5580, it changed the name of theinternal wrapper that Sphinx sees.Since we already ignore `numpy.float64` missing references for the samemethod, add the new name and new class to ignores as well.
And drop the manual wrapper to emulate it.
This is the recommended, but not-yet-default, holder for C++ classes.
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