gistfile1.js

const getPosition = (position = 0) => {
  return {
    x: 0 + position,
    y: 0 + position,
  }
};

const parseMessages = (messages) => {
  const parsedMessages = new Map();
  const queue = [Object.values(messages).find(({tag}) => tag === 'labels-start')];

  let count = 0;
  while (queue.length) {
    const currentMessage = queue.shift();

    parsedMessages.set(currentMessage.id, {
      ...currentMessage,
      position: getPosition(count),
    });
    
    const routes = !currentMessage.routes.length ? [] : 
      currentMessage.routes.split('|')
        .filter((id) => !parsedMessages.has(id))
        .map(key => ({...messages[key]}));

    queue.push(...routes);

    count++;
  }

  return parsedMessages;
};

console.log(parseMessages(messages));