public class ... {
    private HashSet<Message> messages = new HashSet<>();

    void init(ConfigurationLoader<CommentedConfigurationNode> localLoader) {
        try {
            TypeSerializerCollection serializers = TypeSerializers.getDefaultSerializers().newChild();
            serializers.registerType(TypeToken.of(Message.class), new MessageSerializer());
            ConfigurationOptions options = ConfigurationOptions.defaults()
                    .setSerializers(serializers);
            CommentedConfigurationNode node = localLoader.load(options);

            this.messages.add(new Message(1, 600, "msg1"));
            this.messages.add(new Message(2, 600, "msg2"));
            this.messages.add(new Message(3, 600, "msg3"));
            this.messages.add(new Message(4, 600, "msg4"));

            node.getNode("messages").setValue(this.messages);

            localLoader.save(node);
        } catch (IOException e) {
            this.logger.warn("Error saving default config!", e);
        }
    }
}

public class MessageSerializer implements TypeSerializer<Message> {

    public MessageSerializer() {
    }

    @Override
    public Message deserialize(TypeToken<?> typeToken, ConfigurationNode value) throws ObjectMappingException {
        int id = value.getNode("id").getInt();
        int interval = value.getNode("interval").getInt();
        String message = value.getNode("message").getString();
        return new Message(id, interval, message);
    }

    @Override
    public void serialize(TypeToken<?> typeToken, Message message, ConfigurationNode value) throws ObjectMappingException {
        value.getNode("id").setValue(message.getId());
        value.getNode("interval").setValue(message.getInterval());
        value.getNode("message").setValue(message.getMessage());
    }

}