The purpose of the WebRoot folder is to model the deployed application. Everything under webroot gets deployed out as a web application. This is commonly called the “Explored WAR format”, please see this tip: http://www.myeclipseide.com/PNphpBB2+file-viewtopic-t-11099.html
The reason for this is that other top-level resources will go into your project, like a /src dir, maybe an optional 3rd part libs that you don’t want deployed, some documentation, etc. The idea is that all this get’s built into the WebRoot somewhere and when you deploy your project, MyEclipse packages up the WebRoot and deploys it.
In your case you have moved artifacts out of the webroot to the top level of your project, so when you deploy, MyEclipse doesn’t see them, how is it suppose to know what you have in those dirs need to be deployed?