Minor Description
The migration tool runs without any output to SystemOutput. It would be good to perhaps output some status info to System Output, and some other info of more importance to SysErr.
For instance, you can probably count on the fact that users have NOT read the manual past the first paragraph which says how to run the tool. So when it comes to a "Document Annotation" and skips it - it would be good to put out a status notice repeating for the user what they are to do about this 
Other useful normal running output could be something like: scanned xxx files, successfully migrated yyy. Files needing additional attention are: (list).