Better info from Migration tool

[Nicklas Nordborg]

The output of the migration tool is somewhat sporadic and not very inconsistent. It should be made to use the log4j logging system in a better way. We should use the various log levels (debug, info, warn, error) to control output.

• debug - output some info about every item transfered, ie. name, BASE 1 ID, BASE 2 ID
• info - ??
• warn - output info if an item couldn't be connected to an optional item, for example, a missing protocol for a sample, etc. A sensible default should be used for missing links.
• error - If an item could not be migrated due to some other problems

The default log level should be warn.