CZI: make sure that SubBlocks are correctly initialized in openBytes

Fixes #11958.

This also fixes an interleaving bug with one of the files in
test_images_good.
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.
cpp: cmake uses embedded version metadata
ant: release target works when run in a submodule

Check for presence of .git, not whether it's a directory.
First round of changing loci_tools to bioformats_package
Change CMake variable name
Minor change in docs of InstallWizard
Fix URL for download
Misc naming changes
Include bf_package.jar in bftools.zip
Update top-level pom.xml to allow building from source packages
Doc suggestions from melissalinkert
Merge pull request #895 from joshmoore/logback-2

Logback 2 (incl. docs)
Merge pull request #890 from melissalinkert/11958

CZI: make sure that SubBlocks are correctly initialized in openBytes
ant: version and shortversion are the same
Merge pull request #894 from rleigh-dundee/zip-build50

Make a buildable source release (5.0)
Fix missing bioformats_package.jar in bftools.zip

The jar was only present locally in the tools directory
since I had a symlink for testing. In the vanilla builds,
this change is necessary to prevent:

```
-rw-r--r-- 1 jamoore jamoore 16277709 Feb 10 20:36 artifacts/bioformats_package.jar
(ome1)jamoore@blue:/opt/ome3/components/bioformats$ ant dist-bftools
Buildfile: /opt/ome3/components/bioformats/build.xml

dist-bftools:
     [echo] ----------=========== bftools ===========----------
     [exec]     zip warning: name not matched: bioformats_package.jar
...

BUILD SUCCESSFUL
Total time: 0 seconds
```
Update copyright years to 2014
Update a couple of missed copyrights to 2014
Update POM version numbers to 5.0.0-rc2