Add initial support for reading BinaryOnly OME-TIFF datasets

This adjusts the type detection slightly so that .companion.ome files
are detected as OME-TIFF, not OME-XML (as this makes finding and reading
the corresponding OME-TIFF files much easier).  Selecting either a
BinaryOnly OME-TIFF file or the corresponding companion OME-XML file
should result in the entire dataset being read.

Fixes #11951.
Catch NPEs when calling getBinaryOnlyMetadataFile
Ignore metadata files with a .tif/.tiff suffix

Some Prairie datasets contain "OME-TIFF" files with a BinaryOnly entry
that points to a different "OME-TIFF", which is not valid.
Fix calls to getBinaryOnlyMetadataFile()
Fix compile on Java 8.

The original code was causing javac to throw an AssertionError. Working
around the labelled break (by using a flag) seems to fix this fine.
Trying to minimize differences against the original code.
jai: Remove commented-out jj2000 breaks
Use latest/bio-formats5.1 redirects
Merge pull request #1136 from melissalinkert/rebased/develop/binary-only

Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)
Install Sphinx using pip instead of apt-get

The Travis build seems to be failing on a bug which has been fixed in
the 1.2.2 version of Sphinx that we currently use in production
Fix downloads link in sidebar to use new redirect
Merge pull request #1270 from sbesson/latest_redirect_5.1

Use latest/bio-formats5.1 redirects
Merge pull request #1261 from rleigh-dundee/jj2000-jdk8

jj2000: Fix compile on Java 8
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1266 melissalinkert 'Analyze: set littleEndian flag correctly' (user: melissalinkert)
  # PR 1268 carandraug 'multiple netpbm fixes' (user: carandraug)
  # PR 1264 melissalinkert 'Prevent an NPE when referencing Image.AcquisitionDate' (user: melissalinkert)
  # PR 1267 melissalinkert 'Volocity: flag most files as being pixels files' (user: melissalinkert)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1245 imunro 'Add reader for PicoQuant .bin files.' (user: imunro)
  # PR 1269 sbesson 'Extend usage of inputParser in Bio-Formats MATLAB' (user: sbesson)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 1265 qidane 'New units' (label: exclude)
  # PR 1252 imunro 'Add Example code or writing Plate data to ome-tiff.' (user: imunro)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1249 PremyslFiala 'ND2 - Bug fixes' (user: PremyslFiala)
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter' (user: melissalinkert)
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (user: LeeKamentsky)
  # PR 1054 qidane 'Additional annotation points throughout the model' (status: failure)
Updating 03d9c5c..87fbabc
Previously merged:
  # PR 1261 rleigh-dundee 'jj2000: Fix compile on Java 8'
  # PR 1270 sbesson 'Use latest/bio-formats5.1 redirects'
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)'

Generated by OME-5.1-breaking-push#71 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/71/)