Updated PHPDoc

__Added to `Mongo_Database` class:__
```
@method array execute( mixed $code, array $args = array() )
@method array getCollectionNames( bool $includeSystemCollections = FALSE )
```

__Updated `Mongo_Database` class:__
```
@method array command( array $data, array $options = array() )
@method MongoCollection createCollection( string $name, array $options = array() )
@method array createDBRef( string $collection, mixed $a )
@method array listCollections( bool $includeSystemCollections = FALSE )
```

Also I removed some trailing spaces

__Updated `Mongo_Collection` class:__

```
@method bool setReadPreference( string $read_preference, array $tags = array() )
```

Also I removed some trailing spaces and typos.

Thank you for your wonderful project!

Best regards,
Sergey Yakovlev