BaseInstance.clean: add a remove_seed_directory boolean argument (default False) to run`cloud-init clean --seed`

Sometimes, we need to nuke the cloud-init on the instance for some integration tests (more specificfically the once-per-instance modules) . See https://github.com/canonical/cloud-init/issues/6885

We can add this argument to BaseInstance.clean so that this method becomes a "nuclear" clean (we will keep the default as false)

Workaround is to execute the execute method `client.execute(["cloud-init", "clean", "--logs", "--seed"])`