Configure maven-shade-plugin to include src/main/webapp
<configuration>
 <artifactSet>
  <includes>
   <include>*</include>
   <include>*:*</include>
  </includes>
 </artifactSet>
</configuration>

<build>
        <resources>
            <resource>
                <directory>src/main/webapp</directory>
           </resource>
        </resources>
</build>