Store actual configuration in instance directory

[jandubois]

Right now the configuration is derived from _config/default.yaml, $INSTANCE/lima.yaml, and _config/override.yaml, but the combined config is not persisted to the instance directory.

This means the limactl ls command needs to re-create this information. If the globabl _config/{default,override}.yaml files are edited after the instance has been created, then the data displayed by limactl ls may be wrong.