Update `pyproject.toml`

[msto]

• [x] Tooling configuration should be moved out of per-tool config files and into pyproject.toml
  • [x] flake8.cfg #140
  • [x] mypy.ini
• [x] dev-dependencies is deprecated and should be replaced with group.dev.dependencies
• [x] Sphinx/doc dependencies should be moved into a docs group