Moved SCIFIO context to ome.scifio FormatTools

Moved the static context to SCIFIO format tools, since it is a SCIFIO
concept.

The loci.formats FormatTools can reference this context so that both
layers have access to the same static context.
Created ome.scifio version of AxisGuesser

Code is almost identical and log --follow still works, thus there is no
need for a two stage commit.
Copied FilePattern/FilePatternBlock to SCIFIO

These classes are almost completely unchanged from their loci.formats
versions, thus a two-stage conversion was not necessary.
Copied NumberFilter to SCIFIO

This class was unchanged, just placed in a SCIFIO package. Thus a
two-stage commit was unnecessary to preserve log --follow performance.
Copied DimensionSwapper to SCIFIO

First stage of converting DimensionSwapper to SCIFIO: a verbatim copy to
a SCIFIO package, to preserve log --follow performance.
Implemented SCIFIO DimensionSwapper

Second stage of converting DimensionSwapper to SCIFIO: added a working
implementation in SCIFIO terms.
Added setDimensionOrder method to FormatTools

The SCIFIO FormatTools class now contains a convenience method for
setting the DimensionOrder on a CoreMetadata object, updating axis
lengths and types as needed given a CoreMetadata object and desired
ordering.
Added a copying constructor for CoreMetadata

Copies of CoreMetadata (and thus CoreImageMetadata) can now be created
by constructing a CoreMetadata object using a desired source.
Added getters for CoreMetadata axes types/lengths

Added methods to allow interrogation of CoreMetadata axis types and
lengths.
Added FormatTools#findDimensionOrder(AxisType[])

Added a lower-level findDimensionOrder method that operates directly on
an AxisType array. The CoreMetadata version delegates to the new
signature.
Added String to AxisType[] FormatTools method

Added a findDimensionList method for converting from Strings to
AxisType arrays. Only the classic Bio-Formats dimensions are currently
supported.
Implemented SCIFIO FileStitcher

Second stage of translating FileStitcher: implemented the ome.scifio
version in terms of SCIFIO components.
Added isFormat(String) to SCIFIO Checker

No reason to force a String, boolean signature. The String-only version
defaults false.

Includes API specification + Abstract-level implementation.
Added getReader() method to SCIFIOReaderAdapter

Added an accessor for the underlying IFormatReader wrapped by
SCIFIOReaderAdapter.
SCIFIOReaderAdapter updates CoreMetadata source

When SCIFIOReaderAdapter updates its attached CoreMetadata object, it
also tries to set the source of that object.
Corrected SCIFIOReaderAdapter image/plane index

SCIFIOReaderAdapter should not return the correct image index and plane
index (in SCIFIO terminology)
Updated FormatTools#getZCTCoords

This method requires both an image and plane index in SCIFIO. This has
been corrected in FormatTools, and all existing invocations of this
method now correctly pass both indices.
Removed hard-coded imglib refs from scifio-devel

The scifio-devel pom was updated to remove the hard-coded references to
imglib version and group id.
Moved SCIFIOFormatWriter metadata instantiation

Instead of parsing new metadata when setting the metadata store,
SCIFIOFormatwriter creates new CoreMetadata during setId calls.
Added DiscoverableHandle annotation

All handles will be converted to SezPoz using the DiscoverableHandle
annotation.