Setting sourceMaps option only works for inline SMs

This is my .babelrc

```
{
  "presets": ["es2015", "stage-0", "react"],
  "plugins": ["transform-decorators-legacy", "transform-runtime"],
  "sourceMaps": true,
  "retainLines": true
}
```

However when running babel source maps are not being generated:

```babel app/ --copy-files --out-dir build```

Adding `--source-maps true` to CLI tool forces SMs to be generated. Is it a bug?