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

Move all tools configuration in pyproject.toml.

Remove no longer needed mypy overrides.

In our tests, we are using some patterns that are not supported by the
`importlib` mode, like importing test modules from one another.

So switch back to the default `prepend` mode, but add the
`consider_namespace_packages` option that was introduced in pytest 8.1
so our `swh` namespace package gets properly detected as such.

For reference, see:
https://docs.pytest.org/en/latest/reference/reference.html#confval-consider_namespace_packages

Unfortunately, this breaks support for pytest <8.1

Which itself switches to pytest-postgresql 5.0, which changes the object
the 'dsn' attribute is on.

It now needs types-click which is indeed a dependency of
swh.core[testing].

- Move 'api/client' to the root
- Move 'api/server' into 'java/server'