ant: release target archives release version metadata

tools/source-archive creates and repacks the source release,
and embeds ant and cmake version metadata in the release.
ant/version.xml conditionally includes ant/gitversion.xml,
overriding the use of git when building from a source
release.  This file will never be present in a source
repository.
CoreMetadata: update copying constructors to initialize Modulo values
Allow one Modulo annotation of each type for every Image

Previously, only one ModuloZ, ModuloC, and ModuloT was allowed across
the board, which meant that multi-Image datasets could not use a
different Modulo definition for each Image.
cpp: cmake uses embedded version metadata
Flex: be more permissive in parsing IFDs and XML

This allows a trailing ">" in the XML block, in addition to forcing more
thorough IFD parsing when the images are stored before the IFDs.

See
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-January/004164.html
ant: release target works when run in a submodule

Check for presence of .git, not whether it's a directory.
Fix tiled TIFF saving when partial tiles will be used

If the image width and/or height are not multiples of the tile
dimensions, then the last tile in each row or column will be smaller
than the others.  This commit prevents an exception when that is the
case.
Restrict direct tile copying to single-tile images
Implement pre-loading for .sdt files in the interest of performance as an option.
Extend pre-load option to allow smaller sub-planes & address format issues.
Further format issues.
Split initialisation of channel & time bin into preLoaded & not.
Update top-level pom.xml to allow building from source packages
ant: version and shortversion are the same
Add JAR file to Bio-Formats MATLAB toolbox and prefix it
Add tools dependency in dist-matlab target
Add new Bio-Formats package JAR
Refactor bfCheckJavaPath() function
Fix unit tests and MATLAB M files
Change default threshold in bfCheckJavaMemory

Trigger warning when runtime memory is equal to minMemory - 64