Bugfix/cli config order

Previously this would break:

```
$ vendor/bin/peridot app/specs/api.spec.php -c app/peridot.php
```

This happens because of how php's `getopt` function works. It does not like other arguments coming before what you defined for it.

This PR introduces a new class that preemptively parses the arguments for configuration values so order no longer matters :)