Bump development tools: mypy, codespell, isort, ...

Move all tools configuration in pyproject.toml.

Remove no longer needed mypy overrides.

Related to swh/meta#5075.

Fix hanging test when executed outside tox.

Related to swh/meta#4960

Related to swh/meta#4959

- pre-commit from 4.1.0 to 4.3.0,
- codespell from 2.2.1 to 2.2.2,
- black from 22.3.0 to 22.10.0 and
- flake8 from 4.0.1 to 5.0.4. Also freeze flake8 dependencies.

Also change flake8's repo config to github (the gitlab mirror
being outdated).

black is considered stable since release 22.1.0 and the version
we are currently using is quite outdated and not compatible with
click 8.1.0, so it is time to bump it to its latest stable release.

Please note that E501 pycodestyle warning related to line length
is replaced by B950 one from flake8-bugbear as recommended by black.
https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#line-length

Related to T3922

This also drops spurious copyright headers to those files if present.

Related to T3812

Enable to check package documentation can be built without producing
sphinx warnings.

The sphinx environment is designed to be used in continuous integration
in order to prevent breaking documentation build when committing changes.

The sphinx-dev environment is designed to be used inside a full swh
development environment.

Related to T3258

This fixes the master build [1]

[1] https://jenkins.softwareheritage.org/job/DLS/job/tests/1210/console

Related to D3899#96289

- blackify all the python files,
- enable black in pre-commit,
- add a black tox environment.

Failing tests is less noisy in development mode.

Related D2082

This is (hopefully) a temporary fix that can be removed as soon as
  https://github.com/pypa/pip/issues/6239
is fixed, probably thanks to
  https://github.com/pypa/pip/issues/988