Restored loci.formats.in.BIFormatReader

Restored the BIFormatReader in loci.formats. This class will become a
delegator to the ome.scifio version.
Updated BIFormatReader to ome.scifio.gui package

The SCIFIO BIFormatReader class is now a part of the ome.scifio.gui
package. Its dependences and dependencies upon it have been updated.
Added getFileName() to RAIS

ome.scifio.io.RandomAccessInputStream now has a getFileName() accessor
method for its protected data member "file". This was necessary for
refactored SCIFIO code.
Corrected Location packing import

ICSParser in ome.scifio.ics was referencing an incorrect Location
package. This has been corrected.
Removed unnecessary @Override annotations

Many imported classes had @Override annotations that were causing
compile errors in Eclipse. These have been removed.
Added context to legacy FormatTools

To facilitate legacy code that will require a SCIFIO context object,
FormatTools was chosen to hold that reference.
Added SCIFIOReaderAdapter

SCIFIOReaderAdapter is a wrapper class for loci.formats.IFormatReader,
which extends ome.scifio.Reader. This allows the adapter to be used in
delegation with method signatures involving the IFormatReader.

Currently the ReaderAdapter is unsupported functionally, but can be
compiled against.
Refactored FormatTools for SCIFIOReaderAdapter

loci.formats.FormatTools was refactored to use the SCIFIOReaderAdapter.
ome.scifio.util.FormatTools was correspondingly refactored to remove all
loci.formats classes, as they are no longer necessary as all operations
will be performed on SCIFIO Reader-equivalents.
Cleaned up loci.formats references

Removed erroneous loci.formats package references from comments in
ome.scifio.* classes.
Refactored AWTImageTools for SCIFIOReaderAdapter

Removed all references to any loci.formats classes from the
ome.scifio.gui.AWTImageTools class.

Refactored the loci.formats.gui.AWTImageClass to wrap IFormatReaders in
SCIFIOReaderAdapters when necessasry, to pass control to the SCIFIO
methods.
Removed loci.formats refs from MetadataTools

Removed all references to loci.formats classes from
ome.scifio.util.MetadataTools.

Refactored the loci.formats.MetadataTools to include the missing
functionality for now. This class will need to be split apart or
completely migrated to the ome-xml component to remove any functional
code.
Updated loci.formats.CoreMetadata

Merged changes from Scifio-refactor to loci.formats.CoreMetadata. This
was just a new constructor that constructs loci.formats.CoreMetadata from
ome.scifio.CoreMetadata.
Added Convert method to CoreMetadata

The loci.formats.CoreMetadata class now has a convert method which
produces an equivalent ome.scifio.CoreMetadata object.
Implemented SCIFIOReaderAdapter

Implemented most, but not all, methods. Some are still unsupported.

See javadoc for information.
Imported SCIFIO intermediary classes

Imported the following classes:
SCIFIOFormatReader
SCIFIOFormatWriter
SCIFIOBIFormatReader

from the refactored SCIFIO branch.

These classes are intermediaries, intended to replace the FormatReader,
FormatWriter and BIFormatReader classes respectively.

Eventually the SCIFIO versions will replace the current versions, as
they all delegate control to ome.scifio analogs.

However, until all formats are converted to SCIFIO components, both sets
of classes must co-exist, with the SCIFIO versions extending the
loci.formats.

NB: any format that is converted to SCIFIO components and is set up to
delegate to that SCIFIO reader should then extend one of these
SCIFIOXXXX classes to ensure complete delegation.
Migrated deferring APNGReader

The loci.formats.in.APNGReader class was imported from the
scifio-refactor branch. It now fully defers control to the
ome.scifio.apng reader components.
Imported ICSReader delegator

Imported the loci.formats.in.ICSReader class from the refactored SCIFIO
branch, which delegates all control to SCIFIO reader components.
Imported example classes from scifio-refactor

The example classes, demonstrating functionality of the various SCIFIO
components and their convenience examples, have been migrated from the
refactor branch.
Added component jars from refactor branch

Imported the sezpoz and imglib2 jars from the refactor branch, necessary
for building SCIFIO via ant.
Updated scifio/scifio-devel build.properties

The ant build.properties file was updated for SCIFIO and SCIFIO-devel
to include the imglib2 and sezpoz libraries.