docs: Correct debugging chapter.

@zcbenz, 

the default app can not process `--debug your/app/` correctly. We need to specify the port explicitly. The `optimist` module doesn't support this usage, it will set `your/app/` as the debug port which leads to `default_app/main.js` run in [wrong branch](https://github.com/atom/atom-shell/blob/master/atom/browser/default_app/main.js#L55).