Question: Is there any system/compiler/SDK/IDE that provides an ability to develop desktop applications using JavaScript?

Answer: 
You can use **[node-webkit](https://github.com/rogerwang/node-webkit)**.

It uses webkit to render the webpage and execute the Javascript, and you will have access to all the Node.js javascript API (reading/writing files, …)
You can use [AppJs](http://appjs.org/)

Build Desktop Applications for Linux, Windows and Mac using HTML, CSS and Javascript. I'm planning to use it too.