As discussed in #2855, using an actual warning instead of the logger
allow users to control what gets displayed via warning filters.

According to #2849, some projects, including important data-science
packages rely on `distutils` when creating custom commands, instead of
extending the ones provided by setuptools.

This change should accomodate this use case, while also warning the
users to migrate.

The inconsistency for the `package_data` configuration in sdists
when `include_package_data=True` in #1461 have been causing some
problems for the community for a while, as also shown in #2835.

As pointed out by
[@jaraco](https://github.com/pypa/setuptools/issues/1461#issuecomment-749092366),
this was being caused by a mechanism to break the recursion between the
`egg_info` and `sdist` commands.

In summary the loop is caused by the following behaviour:

- the `egg_info` command uses a subclass of `sdist` (`manifest_maker`)
  to calculate the MANIFEST,
- the `sdist` class needs to know the MANIFEST to calculate the data files when
  `include_package_data=True`

Previously, the mechanism to break this loop was to simply ignore
the data files in `sdist` when `include_package_data=True`.

The approach implemented in this change was to replace this mechanism,
by allowing `manifest_maker` to override the `_safe_data_files` method
from `sdist`.

---

Please notice [an extensive experiment]
(https://github.com/abravalheri/experiment-setuptools-package-data)
was carried out to investigate the previous confusing behaviour.

There is also [a simplified theoretical analysis]
(https://github.com/pyscaffold/pyscaffold/pull/535#issuecomment-956296407)
comparing the observed behavior in the experiment and the expected
one. This analysis point out to the same offender indicated by
[@jaraco](https://github.com/pypa/setuptools/issues/1461#issuecomment-749092366)
(which is being replaced in this change).

* needed for 'License-File' metadata, as this is written
  before MANIFEST is read

This reverts commit ef457b2e4eb215ab9d730afbd61a10ed3b118d3c, reversing
changes made to d2b1f7ebd6ebd57b4a50bc6660e93b31129bacb4.

Enable McCabe complexity check in flake8