Split end user console output from developer output

At the moment most console output is meant for end users, using progress indication and a low volume of messages. With the code base growing more complex, logging output is necessary for troubleshooting purposes by PanTools developers and end users. The optimizations to build_pangenome make liberal use of logging, cluttering the output and making it difficult for end users to figure out what is going on.

It would be best to provide a simple console UI to end users, like we have now, and provide logging to a separate file. In case of errors, or if developers or end users need a more detailed look at PanTools, this log file can be inspected.

Logging should be standardized, e.g. with Log4j2.