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.
MetadataStore: Restore and deprecate setRoot(Object)
ome-xml: Add copy constructor to generated model classes
OMEXMLMetadataRoot: Add copy constructor

Allow instantiation from an existing OME Model object.  This
permits OMEXMLMetadataImpl to continue to allow setting of
OME objects with setRoot, and wrap them automatically.
MetadataTools: Correct checks for OME metadata
merge develop -D org -I include -E exclude: PR 505 (Add MetadataRoot to MetadataStore getRoot/setRoot interfaces)
merge develop -D org -I include -E exclude: PR 521 (Assorted bug fixes for May)