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).
Moved ICS, APNG readers to loci-legacy

The delegating loci.formats.in APNG and ICS readers have been moved to
loci.formats.in within the loci-legacy component.

From this point on, delegating code will be moved to loci-legacy whenever
possible (i.e., when there are no unconverted classes within the scifio
component still depending on that class).
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.
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.
Updated auto-generated delegators

The auto-generated OME-XML classes in loci.formats.meta and
loci.formats.ome have been updated based on the latest delegator
templates (passing control to their ome.xml.meta equivalents).

Templates from:

github.com:hinerm/openmicroscopy.git
   8e9d70a9f2a079e0bfd0b875405cd35de5753557
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.
OmeisImporter operates on loci.formats classes

Fixed a compile error in OmeisImporter regarding the convolution between
legacy delegator classes and refactored live classes.

OmeisImporter will operate exclusively on loci.formats.IFormatReader
objects for the time being. This is due to its dependency on the Reader
wrapper extensions, such as ChannelSeparater, ChannelFiller and
fileStichter - which do not have SCIFIO equivalents.

Once those classes are converted, OmeisImporter should be refactored out
of loci.formats imports and the delegators in those classes should use
the ReaderAdapter class to delegate.
Copied OMEXML services to ome.xml.services

Created a copy of OMEXMLService and its Impl class in ome.xml.services.
The originals in loci.formats.services will remain and become delegators.
Migrated OMEXML Translation classes

Added the necessary classes for translation to OMEXML from the currently
supported SCIFIO formats, including a base OMEMetadata.

Note these translators are not yet fully functional.
Ordered inner classes within formats

Organized the inner classes within each Format into a more natural
progression.
Migrated APNGWriter

Updated loci.formats.out.APNGWriter with a refactored SCIFIO delegator.
Moved loci.formats.APNGWriter to loci-legacy

As the APNGWriter is a deprecating class with no dependencies, it
belongs in the loci-legacy component.
Updated copyright header for SCIFIO classes

The copyright header has been added/updated for all migrated SCIFIO
classes.
Bug fix: CoreMetadata convert method

loci.formats.CoreMetadata's conversion method, to generate
ome.scifio.CoreMetadata, now properly sets each axis length, and sets
the total number of planes.
AbstractReader sets current filename

AbstractReader now uses its pre-existing currentId variable by setting
the current file name whenever the source is set.
Bug fix: FormatTools

ome.scifio.util.FormatTools now properly passes plane counts instead of
image counts for several methods.

Additionally, when checking plane parameters, the file id is verified
instead of the stream, to allow for fake file checking (which currently
can not have a RandomAccessxxxStream instantiated)
Corrected CoreMetadata planeSize calculation

Multiply planes instead of adding them.
Added sezpoz and imglib to loci-plugins build.prop

The loci-plugins ant targets will now include the sezpoz and imglib on
the classpath, which was necessary for scifio dependencies.