flush console before running diff count in geogig-add
Fix a bug in DiffTree by which the producer thread may never finish.

It can happen if the consumer hasn't been called at all because
the filtering decorators filtered everything. Setting the finished status
in the finally clause fixes the issue.
Add a couple shortcuts to avoid moving objects that already exist when committing.
make RevTreeBuilder load all missing buckets in one shot
Make GeoGigFeatureReader clip query bounds to dataset bounds
Move ConnectionManager to core
remove unintended System.err.println call