foo.js

var fs = require('fs');
fs.readdir('./challenges/',function(err,files){
  
  if(err) throw err;

  for(i=0;i<files.length;i++) {(
    function(index) {
      fs.readFile('./challenges/' + files[index], "utf-8", function (err, data) {
        if (err) throw err;
        challenges.push({ 'id':j, 'markup': marked(data) });
      });
    })(i);
  }
});