Handle scenario where scanned item is filtered out

BATCH-2302 documents a scenario where an item throws an exception in a
fault tollerant step in the write, then in the process, throws an
exception as well.  This leads to an infinite loop.  To address this,
prior to attempting to write items during scanning we need to validate
that the there are items to be written (we were not which was causing a
NoSuchElementException when we did inputs.next().

This commit also removes an eronous System.out left in the
CoreNamespaceUtils.
Update javadoc to remove javadoc warnings
Ignoring tests that I had unignored