Added image, plane index to getColorTable

The HasColorTable API can now specify the image and plane index of the
desired ColorTable.
Added Parse signature to JPEG2k Parser

As the JPEG2000 format has been replaced by the JPEG2000Format.Parser,
added a parse(RAIS, Metadata, long maxOffset) signature to support the
same functionality as the legacy parser.
Adjusted ByteArrayPlane construction

A byte array is now allocated by using FormatTools.bytesPerPixel for the
pixel type, instead of directly dividing the bits per pixel by 8 (as
there can be bits per pixel that aren't evenly divisible by 8).
Refactored translator naming

The OME translators have now been consolidated to a single class, of the
non-ome name (e.g. "APNGTranslator"). These classes are containers for
one or more nested class that perform the actual translation.
Converted TIFFJAI Format

The loci.formats TiffJAIReader was converted to SCIFIO components in
ome.scifio as TIFFJAIFormat.
Converted MinimalTIFF Reader

Translated the loci.formats MinimalTIFF reader to SCIFIO components in
ome.scifio, as MinimalTIFFFormat. Supporting classes (TiffParser and
TiffCompression) were updated as well, and the scifio Codec interface
was marked as Contextual (the abstract codec heirarchy already extended
AbstractContextual, but MinimalTIFFFormat required Codecs to guarantee
context).

The TIFF/BaseTIFF/OME-TIFF heirarchy will be preserved via intra-format
dependencies on specific components.
Converted TIFFFormat

The loci.formats TiffReader and TiffWriter were consolidated to SCIFIO
components in ome.scifio as TIFFFormat. The supporting TiffSaver was
also copied to SCIFIO.

As TIFFFormat extended BaseTiffReader, it was also marked deprecated
(although its logic is restricted to a BaseTIFFParser in the new
TIFFFormat).

The TiffDelegateReader was also marked deprecated although it should
still function as normal.
Converted OME-TIFF format

Translated the loci.formats OMETiffReader and Writer to SCIFIO
components in ome.scifio, consolidated to the OMETIFFFormat.

Added required "getOriginalMetadata" method to OMEXMLService as well.
Removed Bio-Formats from the Conversion test cp

Some Bio-Formats readers were superceding OME-TIFF for testing.
Eventually the test-suite should just be refactored for SCIFIO
specifically.. for now, BF is just removed from the CP for this test.