Fix up tests after repo reorganization

Fix the default tox configuration so it works properly if a developer
just runs "tox" on their local system by removing environments from the
default list that do not exist. Add the jjb environment to the list.

Add the missing argument to check_projects_yaml_alphabetized.sh and
remove the unused arguments from run-layout.sh.

Exclude the .test directory created by the zuul test environment from
the files checked by flake8.

Change-Id: I72cb9aa3908d16f9e5b6d6445b07819563ce9104
Merge "Fix up tests after repo reorganization"