Fix dangling file handles when using BF methods

Previously, with virtual stacks disabled, calling BF.openImagePlus or
BF.openThumbImagePlus would result in reader.close() never being called,
which eventually resulted in too many open files.
Merge pull request #46 from melissalinkert/build-fixes

Build fixes
Add real support for MJPEG AVI files

The critical differences between MJPEG and JPEG are:

  0) MJPEG uses a fixed Huffman table, but this table is never stored in
     the JPEG codestreams.
  1) MJPEG data is always YCbCr, so must be transformed to RGB after
     decompressing.

Closes #5918, closes #8224.
Use new safe multiplication method to find > 2 GB planes
Add support for multi-position MicroManager data

Closes #8208.
Do not populate the detector voltage

In the context of Leica LIF, the voltage is evidently meaningless.

See #8306.
Strip out all but the first application marker

As noted in the comments, ImageIO tends to complain if there are
multiple application markers.

Reported by Colin Blackburn.
Add support for JPEG-compressed Canon DNG files

Reported here:

http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=1077
Look for the channel count in one more place

This only affects files created with Elements 4.0.

Reported by Marek Basler.
Ignore corrupt lossless-compressed planes
Prevent potential NPEs with 0-indexed files

This should fix a bunch of failures reported by the
"BIOFORMATS-full repository test" on OME Jenkins.
Add support for writing uint32 JPEG-2000 data

Closes #8226.

To test, verify that pyramids are correctly generated for a uint32 big
image imported into OMERO.
Disable file (un)grouping options when reading from OMERO

Closes #8302.

To test, verify that "Group files with similar names" and "Open files
individually" are unchecked and greyed out when viewing an image via
Insight as an ImageJ plugin.
Ignore last part of channel name when building file lists

If the channel name is "xxx-yyy", then we ignore the "-yyy" as it won't
actually be in the TIFF file names.  The channel name will still be
populated as "xxx-yyy".

Reported by Kally Pan.
Scale 8-bit LUT values up to 16 bits

We need to return 16-bit values, even though only 8 bits per channel are
stored for the LUT.  So we just multiply each value by 257 to get new
values in the range 0 - 65535.

Noticed by Stéphane Dallongeville.
Fix TiffData population when writing a subset of planes

If we are only writing part of the original dataset to OME-TIFF (e.g.
with the '-channel c' option to bfconvert), then there cannot be any
gaps in the plane indices passed in calls to setTiffData* and setUUID*
in MetadataStore.

Reported by Simon Blanchoud.
Be more permissive in detecting Prairie datasets

We now no longer require the .cfg file to be present, and allow an extra
"_" in the .xml file name.
Add retrotranslator dependency to the SCIFIO POM
Merge remote branch 'curtis/bf-close-fix' into sprint11-bug-fixes
Ensure that wrapped ImagePlus objects will be closed

CompositeImage does not propagate calls to close(), so any ImagePlus
objects that were wrapped in a CompositeImage were not closed.  This
caused file handles to remain open when the ImagePlus objects were
instances of VirtualImagePlus.

Now, we override CompositeImage.close() so that the wrapped ImagePlus is
closed as well.

Reported by Stephan Preibisch.