Implemented SCIFIO DelegateReader

Second stage of DelegateReader conversion. Implemented in SCIFIO terms.
Implemented SCIFIO ChannelSeparator

Second step of converting ChannelSeparator: implemented in SCIFIO
context.
Moved coreMeta method to ReaderWrapper

Moved the helper method: coreMeta from ChannelSeparator to
ReaderWrapper. This methid accesses the CoreMetadata object of the
wrapped Reader and could potentially be useful to many ReaderWrappers.
CoreMetadata: set individual axis length/types

Added methods to CoreMetadata in SCIFIO to set individual Axis lenghts
and types, instead of having to provide an entire array. This helps to
facilitate swapping classes like DimensionSwapper without being overly
cumbersome.
Implemented SCIFIO ChannelFiller

Implemented the ome.scifio.wrappers ChannelFiller in SCIFIO terms.
fix: moved SCIFIO context to ome.scifio FormatTools
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.