Feature/logging info

Hello John,

I've added some code to do logging using [log4j](http://logging.apache.org/log4j/1.2/index.html) which should hopefully make it easier to debug exactly what's going on whenever Galaxy bootstrap is running.  The logging level can be adjusted by modifying the file `src/main/resources/log4j.properties` or creating your own properties file and passing it in on the command line.

Aaron