How to flatten multiple nested node readline questions?

Flow Control libraries such as Async.js exist for exactly that. With async, your code can become:

var async = require('async');
var prompt = chalk.bold.magenta;
var info = {};

async.series([
    (callback) => {
        rl.question(prompt('Thing One : '), function(args) {
            info.one = args;
            callback();
        }
    },
    (callback) => {
        rl.question(prompt('Thing Two : '), function(args) {
            info.two = args;
            callback();
        }
    },
    (callback) => {
        rl.question(prompt('Thing Three : '), function(args) {
            info.three = parseInt(args);
            callback();
        }
    }
], () => {
    rl.close();
    runSomeOtherModuleNow();
});