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
IFormatReader: Remove unused getMetadataStoreRoot method

This method returns an Object, so is not useful unless the
specific type is known in advance.
Fix OME-XML metadata creation in bfGetReader & bfsave functions
OMEXMLService: convertMetadata only works with OMEXMLMetadata
OMEXMLService: Remove isOMEXMLRoot and isOMEXMLMetadata

These are easily checked with instanceof.
MetadataStore: Move getRoot and setRoot to OMEXMLMetadata

getRoot and setRoot in MetadataStore work with plain Objects.
This means they are useless unless you know the concrete type
being returned.  This patch moves the methods to OMEXMLMetadata
and makes them use OME root node objects.  Existing users of
getRoot or setRoot now cast their MetadataStore object to
OMEXMLMetadata and then call the methods using this interface,
making all usage type-safe.  This also requires changing the
types in use in a number of other places to avoid unnecessary
casts.