Kevin,
But I want to know why you guys designe MyEclipse to do that.
The default project structure in MyEclipse is that of an exploded WAR file, however your source code should NOT be deployed with your application, so we moved the WAR-structure down one level into its own folder (default name is “WebRoot”) and allow people to setup their project one level above that, for example, add /src folders, /docs folders, /lib folders, etc… anything else they need for the project that doesn’t need to be deployed with the WAR file.
MyEclispse create classes folder automatically under WEB-INF folder under WebRoot folder…..
This is defined by the web application spec, your class files must go into WEB-INF/classes, your JAR must go in WEB-INF/lib… both are recognized by MyEclipse as special and treated accordingly.
I also would like to know whether it is fine for adding resources folder under src folder to add application.properties
Yes you are exactly right, they should go in your /src tree. Eclipse will copy them over into the output folder (WEB-INF/classes) when your project builds.
And is there a way to add build.xml to be used with Ant?
Sure, just drop it in the root of your project, at the same level with /src and /WebRoot… this is typical project setup.