Have you tried using war packaging? Have you noticed what Maven does when you do so? I am tempted to tell you, but I think that you need to try it for yourself. After you run the build (mvn package), closely examine the target directory and tell me what you see.
Important points:
* a Maven build never modifies anything in the "src" directory.
* all "built" artifacts go into the "target" directory
* this does involve a lot of file copying, especially for static web resources, but it does facilitate filtering those static resources
* the "packaging" value describes not just the final artifact type, but also defines the directory structure and the steps used to build the project.
Also, you might be interested in looking at some of the options provided by the War plugin:
http://maven.apache.org/plugins/maven-war-plugin/
And some excellent reading:
Better Builds With Maven:
http://www.maestrodev.com/support
Maven: The Complete Reference:
http://www.sonatype.com/index.php/Support/Books/Maven-The-Complete-Reference