Micromanager: use full channel name in file names when necessary

If the trimmed name (everything before the first '-') is not sufficient
for picking up TIFF files, then use the full channel name.  I suspect
this is only an issue for datasets produced with older versions of
Micromanager, but that may not be correct.
MM: trim the timepoint count if all files are missing beyond a certain point

Fixes ticket #11972.
Micromanager: do not allow Position to query reader state in openBytes

This prevents potential exceptions when openBytes is called on a
memoized file.
Merge pull request #1014 from bpindelski/jpegxr

Add initial structure for decompressing JPEG XR images (assist #8493).
Check ABSTRACT_PROPRIETARY_OVERRIDE on creation
Update import of OMEXMLMetadataRoot in test
Merge pull request #1057 from melissalinkert/windows-tests

Fix file handle/line ending issues so that tests pass on Windows
Update auto-generated documentation

Repository: openmicroscopy/bioformats
Already up-to-date.

Generated by BIOFORMATS-5.1-latest-docs-autogen#57 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-latest-docs-autogen/57/)
Updating asXMLElement Java template
Updating copyright year
Updating C++ templates
Merge remote-tracking branch 'origin/develop' into new-annotation
Merge pull request #1065 from snoopycrimecop/autogen/develop/latest

Update auto-generated documentation
Merge pull request #1063 from melissalinkert/rebased/develop/micromanager

Micromanager fixes (rebased onto develop)
DICOM: expand sequence reading to include known sequences

See QA 9184.
Exclude one non-sequence tag from sequence parsing
Merge pull request #1055 from rleigh-dundee/fix-poms-develop

Fix up Bio-Formats POMs (rebased)
docs: Delegate all sphinx Makefile targets to ant
Merge pull request #1073 from rleigh-dundee/ant-makewrap

docs: Delegate all sphinx Makefile targets to ant
Remove dead link