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.
Converted SCIFIO Reader to single classes

The SCIFIO ICS and APNG reader component sets have been converted to a
single class (the concrete Format) with nested classes.

All classes should be accessed through the Format's creator methods.

These changes are also reflected in the delegating classes
(SCIFIOFormatReader and its APNG/ICS extensions in loci.formats).
Created ome.xml.meta package in scifio

loci.formats.ome and loci.formats.meta have been migrated to
ome.xml.meta.

This is a placeholder package, in terms of being in the scifio
component. Eventually the goal is to move this to the ome-xml component,
when the dependency between scifio and ome-xml can be reversed.
Moved missing-ome-xml test to scifio-devel

As scifio-devel has acquired an OME-XML dependency, it no longer makes
sense for the downstream scifio component to have the missing-ome-xml
test (as ome-xml.jar will always be present on the classpath
transitively through scifio-devel.jar).

Thus this test was moved to scifio-devel.
Updated auto-generated classes

Updated the auto-generated ome-xml Metadata classes based on updated
templates from:

github.com:hinerm/openmicroscopy.git
  8e9d70a9f2a079e0bfd0b875405cd35de5753557
Removed IMetadata import from OMEXMLMetadata

ome.xml.meta.OMEXMLMetadata no longer needs to explicitly import an
IMetadata, as they are located in a common package.
Converted loci.formats.ome.* to delegators

The classes in loci.formats.ome were all converted to delegators,
passing control to their ome.xml.meta equivalents.
Converted loci.formats.meta.* to delegators

All non-autogenerated clsses in loci.formats.meta are now legacy
delegators which pass all control to their ome.xml.meta equivalents.