In general for a Java-based Maven project, non source files should go in the src/main/resources sub-directory of the project. The contents of the resources directory are copied to the output directory (by default target/classes) in the process-resources phase of the build.
For war projects it is slightly more complicated, there is also the src/main/webapp directory, where Maven expects to find WEB-INF/web.xml. For your war to build that file must exist or you'll see an error message like this:
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Error assembling WAR: webxml attribute is required (or pre-existing WEB-INF/web.xml if executing in update mode)
As the WEB-INF direcory must exist under src/main/webapp, I'd recommend avoiding defining it again in src/main/resources. Although this is perfectly valid and the contents of the two directories will be merged, it can get confusing if a file is defined in both. The contents of src/main/resources will take precedence as they are copied over the top of the contents from src/main/webapp