fix(cli): convert capabilities arguments to dot-notation for WebDriver compatibility

WebDriver requires capabilities properties to be written in dot-notation, like when specifying the path of PhantomJS for instance:

```
capabilities: {
  'phantomjs.binary.path': 'node_modules/phantomjs/bin/phantomjs'
}
```

But when setting this path using the command line like this:

```
protractor --capabilities.phantomjs.binary.path node_modules/phantomjs/bin/phantomjs
```

`cli.js` converts this setting to a nested object:

```
{  capabilities: 
   { browserName: [ 'phantomjs', 'phantomjs' ],
     phantomjs: { binary: [Object] }
```

The nested object doesn't get interpreted, so PhantomJS can't be executed.

It's highly desirable to be able to configure Protractor entirely by a command-line command as Protractor gets configured that way by tools like Grunt. Currently that's not possible though due to this limitation.