fix: set __file__ on submodules (#5584)

* fix: set __file__ on submodules

The docs state ['The caller is responsible for setting a `__file__` attribute'](https://docs.python.org/3/c-api/module.html), but we
were not doing that, which interferes with pickling objects in submodules using cloudpickle. Users previously had to set the `__file__` attributes manually,
such as in https://github.com/scikit-hep/boost-histogram/blob/1fbbe1632e1665863b9c84b10edf6aa659a14bf1/src/boost_histogram/histogram.py#L83-L90.

Signed-off-by: Henry Schreiner <henryschreineriii@gmail.com>

* fix: support GraalPy

Signed-off-by: Henry Schreiner <henryschreineriii@gmail.com>

* fix: workaround only for GraalPython

Signed-off-by: Henry Schreiner <henryschreineriii@gmail.com>

* Add GRAALPY_VERSION_NUM to GraalPy workaround

* Fix "GRAALPY_VERSION_NUM not defined" issue

```
/Users/runner/work/pybind11/pybind11/include/pybind11/pybind11.h:1340:32: error: 'GRAALPY_VERSION_NUM' is not defined, evaluates to 0 [-Werror,-Wundef]
                               ^
```

Related ChatGPT conversation: https://chatgpt.com/share/67e6cb99-84b0-8008-99d6-aadc70242cf3

---------

Signed-off-by: Henry Schreiner <henryschreineriii@gmail.com>
Co-authored-by: Ralf W. Grosse-Kunstleve <rgrossekunst@nvidia.com>