Checkstyle and logging improvements
- Added Checkstyle configuration files (checkstyle.xml and checkstyle-suppressions.xml). Both are modified versions of the ones from the ConceptWiki project (see https://trac.nbic.nl/conceptwiki/browser/trunk/code/conceptwiki).
- Resolved all sorts of Checkstyle issues: added Javadocs, hidden constructors, reordering import statements, and package-info.java files for two packages.
- Used logging instead of println statements in several classes and switched to the simple logging facade for Java (SLF4J) instead of Log4j.