Investigate making the setup scripts handle alternate directory layouts

[deviantintegral]

drupal-admin-ui had to make some changes to the scripts to work with how they have their modules in the repository. As is, we expect:

• One module per repository
• Or, straight submodules, with the parent composer.json containing all submodule dependencies.

The biggest gap is that we currently only allow one call to update-dependencies.sh. There's likely similar limits hiding in the test suites too.

Let's see if there's an easy way to handle all of these cases, or if we should just document it as a "make your own customizations" type of problem.