Extensions are loaded with default options

In loaded extension there is no access to config by options in console. 

For example:

```
$this->output->getVerbosity()
```

always return '1' even if script is started with '-vvv'

As I found in https://github.com/Codeception/Codeception/blob/master/src/Codeception/Codecept.php#L65 extensions are loaded before merging config from file and constructor parameter.
