I tried to build the showcase and there's an error with the resource filtering build participant. It doesn't like that you defined absolute targetPaths (starting with "/") for webresources. I made it work using :
<webResources>
<resource>
<directory>src/main/webapp</directory>
</resource>
<resource>
<directory>src/main/webapp-tomcat</directory>
</resource>
<resource>
<directory>src/main/java</directory>
<targetPath>WEB-INF/src</targetPath>
</resource>
</webResources>
You can check the content of the web-resources folder under the "Deployed Resources" node, in the Project Explorer.
This is definitely a m2e-wtp bug.