GRE-404 Fixing final configuration file loading problems

= moved application.conf to src/main/resources, more intuitive, plus will be picked up when running form the IDE
= excluding this from target jar (see pom)
= removing loading rpki-validator.conf from classpath in main in dev mode, no longer works this way
GRE-404 Set up logging programmatically for CLI. The log4j.xml was conflicting with rpki-validator-app.