CLI tests are flaky from CDK-796

CLI tests are flaky from the addition of CDK-796, which updates the CLI run method so that it sets its Configuration as the global default with DefaultConfiguration.set. This is correct for the CLI because there's only one entry point. There are two problems from this:
1. Some tests use the CLI for setup, e.g., creating schemas with csv-schema
2. Some tests don't configure main with a Configuration, so DefaultConfiguration is null

Because this is global state, behavior depends on the order in which tests run. To fix this, we need to pass the same Configuration for test suites and check that the configuration from getConf() in main is not null before setting it as the default.