How do I run the system commands in javascript?

Please give more information of your environment.

Unprivileged JavaScript in a browser can neither list files nor execute programs for security reasons.

In node.js for example executing programs works like this:

var spawn = require('child_process').spawn,
var ls  = spawn('ls', ['-l']);
ls.stdout.on('data', function (data) {
   console.log(data);
});

And there is a direct way to list files using readdir()

An even easier way in node.js is:

var fs = require('fs');
var ls = fs.readdirSync('/usr');

The variable ls now contains an array with the filenames at /usr.

You can't run system commands on the client with JS since it works inside a browser sandbox. You'd need to use some other client side tech like Flash, ActiveX or maybe Applets