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.