Restructure folders to comply with standards and make tests run on CI-Server

I updated the POMs and the folders to use src/main/java/xxx and src/test/java/yyy for source and test files. Now running ```mvn test``` and ```mvn install``` includes all three modules.

The .project and .classpath files may be broken.

@fruetschi: Please look at my changes and merge the Pull Request if the change is for ok you (and the PR build passes)