Add missing type hints & Force type hints - Part 3 (#4805)

* add typehints to tests.publishing

* add typehints to tests.puzzle

* add typehints to tests.repositories

* add typehints to tests.utils.test_authenticator, tests.utils.test_env, tests.utils.test_env_site, tests.utils.test_exporter

* add typehints to tests.utils.test_extras, tests.utils.test_helpers, tests.utils.test_password_manager, tests.utils.test_patterns, tests.utils.test_pip, tests.utils.setup_reader

* add typehints to tests.test_factory

* add typehints to tests.helpers

* add remaining missing typehints to tests.conftest

* add flake8-annotations to flake8 pre-commit hook

* create a FixtureDirGetter protocol type

* add comments to .flake8 settings and fix missing typehints after rebase