swh-pipeline: Execute all code quality checks instead of just flake8

Prefer to rely on pre-commit to run all code quality checks in order to also benefit from black, codespell and isort checks.

This will enforce newly introduced code to pass those checks and force external contributors to install the pre-commit hooks.

I tested the changes in docker and also processed all swh repositories to fix failing checks after the recent version bumps of code quality tools in pre-commit configuration.