Fixes for bug 1112084 and some doc changes

All the dev requirements have been specified in requirements/dev.txt and are installed while the VM is provisioned. Docs have been updated for the current pre-commit hook. The users no longer have to install flake8 manually.
@willkg said this on #input "we should install it with pip--not peep. that way we get dependencies. we don't really care about making sure what we are installing is exactly what we installed last time for dev libraries.". So I guess, I could remove the hashes and probably the version numbers as well.