Streamline logging

[lenhard]

This pull request streamlines the usage of logging APIs in JabRef. All direct usages of java.util.logging are now replaced by usages of commons.logging. Internally, commons.logging is configured to default to java.util.logging, so nothing is fundamentally changed. java.util.logging is still needed in a single class, CacheableHandler, to access the actual log for display in the UI. This is not possible directly with commons.logging and requires the usage of the underlying logging API.

The major benefits are of this pull request are:

• All classes use the same mechanism for logging
• Many log messages have been checked and improved if possible
• It is now easier to switch out the internal logging implementation

[simonharrer]

shouldn't this be LOGGER.warn instead of LOGGER.debug?

[lenhard]

The log levels and practices of commons.logging and java.util.logging are somewhat different. Since I converted the whole thing to commons, I tried to follow their guidelines. In many cases, such as the above, it is quite hard for me to decide the criticality of the event, and, hence, the log level. If you know that this event is really that critical, it is no problem to change the logging. Should I do that? Perhaps ``LOGGER.error` would also be appropriate?