move from log4j to log4j2

One of current dependencies (jsbml) is using newer version of log4j (2.3). This new version is "in conflict" with our log4j version (1.17). As a result our configuration is ignored during logging.

For now as a workaround (!200 (merged)) we excluded manually log4j2 dependencies and everything seems to work, but it should be changed to log4j2 at some point.