If you want to start with a Java EE web application, you can simply use the maven-archetype-webapp archetype to generate the Maven project skeleton, which is shown as follows:

$ mvn archetype:generate -B
                   -DgroupId=com.packt.samples
                   -DartifactId=my-webapp 
                   -Dpackage=com.packt.samples.webapp 
                   -Dversion=1.0.0  
                   -DarchetypeGroupId=org.apache.maven.archetypes  
                   -DarchetypeArtifactId=maven-archetype-webapp 
                   -DarchetypeVersion=1.0

The preceding command will produce the following directory structure. One issue here is that it does not have the java directory just after src/main. If you want to add any Java code, you need to make sure that you first create an src/main/java directory and create your Java package under it. Otherwise, with the default configuration settings, Maven won't pick your classes for compilation...