Call updateObjects/updateReferences in a loop

This prevents Ice.MessageSizeMax from being exceeded when there are many
objects to update.  The default is to only update 2000 objects or
references at a time, though this could be made configurable.

See https://trac.openmicroscopy.org.uk/ome/ticket/11990

To test files are needed that insert a vast number of rows into the DB. The recent files from @dpwrussell did this. A fake file of the form ... will also work.