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
Cleaned up loci.legacy.adapter package

Removed unnecessary methods, added and corrected javadoc, fixed compiler
warnings.
Cleaned up loci.legacy.context package

Added javadoc to the LegacyContext
Cleaned up loci.common.* legacy packages

Cleaned up loci.common, loci.common.adapter, loci.common.enumeration and
loci.common.xml packages. These were done together because changes in
some packages affected other packages as well. All affected classes were
delegators or adapters between legacy and modern classes.

Converted many classes that effectively were Wrappers to implement the
Wrapper interface. Removed unnecessary/dangerous methods, including
Object overrides. Added more javadoc. Added deprecation annotations.