Clean up: ome.scifio package

Update the javadoc and code style of all classes in the ome.scifio
package.
Removed MetadataHandler

This class is not referenced anywhere any more, and is completely
necessary. Thus it is being removed.
Cleaned up ome.scifio.filters package

Added and corrected javadoc, consolidated repeated methods, removed
unused methods.
Cleaned up ome.scifio.formats package

Fixed and added comments, simplified code and reduced repeated
statements.
Cleaned up ome.scifio.gui package

Added comments and missing headers.
Moved LocationService to ome.scifio.services

Consolidating all SCIFIO services to a common package.
Moved OMEXMLMetadataService to ome.xml.services

Consolidating the OME-XML services to a single package.
Cleaned up ome.scifio.io package

Updated javadoc, removed excess whitespace.
Renamed findSeriesPatterns to findImagePatterns

"Series" was a naming convention of Bio-Formats. In SCIFIO the
equivalent is "Image".
Cleaned up ome.scifio.services package.

Updated and added documentation. Pruned unused API.
Cleaned up ome.scifio.util package

Added and updated javadoc. Clarified method signatures.
Cleaned up ome.xml.meta package

Fixed compiler warnings. Cleaned up comments.
Cleaned up ome.xml.services package

Updated javadoc and formatting issues.
Cleaned up ome.xml.translation package

Expanded and clarified javadoc.
Cleaned up loci.formats package

Added and corrected javadoc. Removed methods without a backing
interface. Clarified documentation. Cleaned up @Deprecated annotations.
Cleaned up loci.formats.gui package

Clarified @deprecation usage.
Cleaned up loci.formats.in package.

Clarified deprecation. Removed unnecessasry methods.
Cleaned up loci.formats.out package

Clarified deprecation.
Cleaned up loci.formats.ome package

Added deprecation tags to OmeisImporter
Cleaned up loci.formats.codec package

Added deprecation annotations to CodecOptions