DICOM: fix file grouping so that path names are normalized

On Windows in particular, the list of pattern files often has extra path separator escaping, which prevents the
pattern files from being matched with the files from the directory listing.
Merge pull request #999 from melissalinkert/sdt-mode-13

Fix for single channel  meas_mode 13 data (rebased onto develop)
Merge pull request #1029 from melissalinkert/rebased/develop/11850

TIFF: adjust optimal tile height if tiles have height of 1 (rebased onto develop)
Merge pull request #1030 from melissalinkert/rebased/develop/czi-fixes

CZI: restrict dimension adjustment (rebased onto develop)
Merge pull request #1031 from melissalinkert/rebased/develop/volocity-timestamps

Volocity: parse timestamps from .atsf files (rebased onto develop)
Merge pull request #1041 from melissalinkert/rebased/develop/template-fix

Minor docs autogen fixes (rebased onto develop)
Merge pull request #1042 from melissalinkert/rebased/develop/dev50/ome-xml-package-bug

OME-XML package bug-fix (rebased onto develop)
Merge pull request #1050 from melissalinkert/rebased/develop/sdt-image-name

Add the series index to the default image name (rebased onto develop)
Merge pull request #1053 from melissalinkert/svs-physicalsize

SVS: store the PhysicalSizeX and PhysicalSizeY attributes
merge develop -D org: PR 857 (Initial support for Zeiss .lms files)
merge develop -D org: PR 858 (Initial support for Veeco AFM data)
merge develop -D org: PR 981 (Ignore namespaces when filling in an XMLAnnotation's Value)
merge develop -D org: PR 983 (Woolz: make sure the service is initialized when calling openBytes (rebased onto develop))
merge develop -D org: PR 1014 (Add initial structure for decompressing JPEG XR images (assist #8493).)
merge develop -D org: PR 1028 (Large fileset performance improvements (rebased onto develop))
merge develop -D org: PR 1049 (DICOM: fix file grouping so that path names are normalized (rebased onto develop))
merge develop -D org: PR 1057 (Fix file handle/line ending issues so that tests pass on Windows)
merge develop -D org: PR 1060 (Allow dist-matlab to run on Windows)
merge develop -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model' (label: exclude)
  # PR 528 melissalinkert 'Tile performance improvements for VMS and NDPI' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1055 rleigh-dundee 'Fix up Bio-Formats POMs (rebased)' (status: pending)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
Updating c8a8cc1..e852f90
Merged PRs (fast-forward):
  # PR 1053 melissalinkert 'SVS: store the PhysicalSizeX and PhysicalSizeY attributes'
  # PR 1050 melissalinkert 'Add the series index to the default image name (rebased onto develop)'
  # PR 1042 melissalinkert 'OME-XML package bug-fix (rebased onto develop)'
  # PR 1041 melissalinkert 'Minor docs autogen fixes (rebased onto develop)'
  # PR 1031 melissalinkert 'Volocity: parse timestamps from .atsf files (rebased onto develop)'
  # PR 1030 melissalinkert 'CZI: restrict dimension adjustment (rebased onto develop)'
  # PR 1029 melissalinkert 'TIFF: adjust optimal tile height if tiles have height of 1 (rebased onto develop)'
  # PR 999 melissalinkert 'Fix for single channel  meas_mode 13 data (rebased onto develop)'
  # PR 1056 rleigh-dundee 'Use ant to build sphinx docs'
  # PR 1058 rleigh-dundee 'source-archive: Close in use files before removing them'

Merged PRs:
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files'
  # PR 858 melissalinkert 'Initial support for Veeco AFM data'
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value'
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)'
  # PR 1014 bpindelski 'Add initial structure for decompressing JPEG XR images (assist #8493).'
  # PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)'
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)'
  # PR 1057 melissalinkert 'Fix file handle/line ending issues so that tests pass on Windows'
  # PR 1060 melissalinkert 'Allow dist-matlab to run on Windows'

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