Add null check
Add AnnotationRef counters to the xsd-fu templates
Add a script for running all of the necessary xsd-fu commands

The BF_HOME environment variable must be set first; this should be the
full path to a working clone of bioformats.git.  Then it is just a
matter of running './xsd-fu-generate', as all of the resulting files
will be copied to the correct location in bioformats.git.
BfPixelsWrapper: do not store the channel count and pixel type
The RGB channel count and pixel type/byte width can vary for every
series, so it is incorrect to store the values for the first series and
use them for every series.

Fixes ticket #10189.
xsd-fu: extend copyright year range to 2013

It was done with the following shell command:

    git grep -l 'Copyright (C) [0-9]\{4\} - [0-9]\{4\}' | \
    xargs sed -i '' -e \
    's/\(Copyright (C) [0-9]\{4\} - \)[0-9]\{4\}/\12013/'
Explicitely specify Markdown extension for VM scripts Readme file
Add source hyperlinks in the VM readme
Fix codeblocks
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 538 (OMERO.tables ArrayColumns #5632)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 558 (Plugin dependencies)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 616 (render_fs_speed_10183)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 620 (Spec clean on dev 4 4)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 639 (Web bugs jan22nd)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 647 (xsd-fu cleanup (dev_4_4))
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 656 (Merge xsd-fu changes from schema-2012-06 (dev_4_4))
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 662 (Cpu)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 666 (Matlab toolbox cleanup)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 668 (Install scc and merge PRs opened against homebrew-alt)
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 684 (BfPixelBuffer/BfPixelsWrapper buffer size fixes (rebased onto dev_4_4))
merge dev_4_4 -D org -I include -E conflict -E needs-fixes -E broken: PR 688 (License updates)