Fix issue #669

Fix for issue #669. Refactor `query` configuration parameter.
Now the right configuration section is the following:

```yaml
propel:
  database:
    connections:
      default:
        settings:
          charset: utf8
          queries:
            - "sql query number 1"
            - "sql query number 2"
```
which is translated into the following php, by running `config:convert` command:

```php
<?php

$manager->setConfiguration(array(
    'settings' => array (
        'charset' => 'utf8',
        'queries' => array(
            0 => 'sql query number 1',
            1 => 'sql query number 2
        ),
    ),
));
```