Introducing slf4j #155

- added runTime scope binding for log4j2 since it's the one logger
framework that was used already elsewhere. We even had already some
config files for it in the structure module
- added the safe config to all poms of modules. Config files for log4j2
are only in the structure module. Other modules will have to add config
files if needed
- default level in config files set to: warn for run, info for test
- moved logging in the PDB parser to slf4j