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
Slidebook TIFF: prevent NPEs when metadata is missing
Slidebook TIFF: close open file handle in TiffParser
PNG: fix support for images with fewer than 8 bits per pixel

Fixes #10887.
Metamorph TIFF: populate PhysicalSizeZ

Fixes #10884.
Leica LIF: parse PhysicalSizeZ from one more place

Fixes #10843.
DNG: fix type checking to prevent picking up Photoshop files
SVS: disable file grouping

It's very common to have similarly-named files in the same directory
that have very different dimensions.  To prevent weird problems with grouping,
and because the workflow of dealing with slides means that grouping
isn't really necessary, it is now disabled.
Slidebook TIFF: make type checking more rigorous
CellWorx: do not pick up .pnl/.tiff files if file grouping is turned off

Noticed by Stéphane Dallongeville.
Leica LIF: a few more physical size and position fixes

Noticed by Olivier Burri:

http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=4710#p9964