Right-click on .js file and then "Debug As -> Node application"
With Node any .js file can be executed. (Hint: this also give you one more way to validate.)
Other debug options were not yet implemented or tested (as ChromeDevTools can give more options, we just have not tried everything, but implemented the most straight-forward ). Play with what you can, raise an issue on github with the error / feature description. https://github.com/Nodeclipse/nodeclipse-1/issues
Be sure that you have read http://www.nodeclipse.org/#support and Online / built-in Help Debug page.