We have 3 new tools that have been added recently. These are Flake8, PHPMD and PHPCS. We will need to update the .yaml config file template and the Config Reference with these new tools.

The .yaml config file template needs these added in the tools section. Refer to the schema for more details.

flake8:
enabled: true
phpmd:
enabled: true
phpcs:
enabled: true

Also add relevant information to the Tools section in Configuration Reference chapter.