Replace use of MetadataTools.createOMEXMLMetadata with OMEXMLService.createOMEXMLMetadata

Since MetadataTools.createOMEXMLMetadata is deprecated, all in-tree
users are hereby converted to use the replacement OMEXMLService
interface.
MetadataTools: Remove deprecated and unused methods
Fix OME-XML metadata creation in bfGetReader & bfsave functions
scifio: Add MetadataRoot interface

This in an abstract interface for the root node of metadata
implementations.
scfio: Add OMEXMLMetadataRoot

OMEXMLMetadataRoot is an ome.xml.model.OME root node, which
also implements the MetadataRoot interface.  It is
constructable using the same signatures as OME.
Use the OMEXMLMetadataRoot and MetadataRoot interfaces

These replace the passing of raw OME objects as Object via
the getRoot and setRoot interfaces of MetadataStore.