I am trying to apply maven to an existing project which already has a directory structure in place. All I can find from previous question is the following.
Maven dir
You can change the default directory structure declared in the Super POM by overwriting them in your pom.
For your example, e.g.
src-java
src-properties
Maven will copy all resources to the jar file. If you want to include WEB-INF to the jar it would be best to move it into the specified resource directory. Otherwise you have to copy it by your own (with maven plugins) to the target directory - I suppose.