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