source-archive: Close in use files before removing them

Required for Windows.
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 999 (Fix for single channel  meas_mode 13 data (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 1029 (TIFF: adjust optimal tile height if tiles have height of 1 (rebased onto develop))
merge develop -D org: PR 1030 (CZI: restrict dimension adjustment (rebased onto develop))
merge develop -D org: PR 1031 (Volocity: parse timestamps from .atsf files (rebased onto develop))
merge develop -D org: PR 1041 (Minor docs autogen fixes (rebased onto develop))
merge develop -D org: PR 1042 (OME-XML package bug-fix (rebased onto develop))
merge develop -D org: PR 1050 (Add the series index to the default image name (rebased onto develop))
merge develop -D org: PR 1053 (SVS: store the PhysicalSizeX and PhysicalSizeY attributes)
merge develop -D org: PR 1056 (Use ant to build sphinx docs)
merge develop -D org: PR 1057 (Fix file handle/line ending issues so that tests pass on Windows)
merge develop -D org: PR 1058 (source-archive: Close in use files before removing them)
merge develop -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)' (status: error)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (label: exclude)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 528 melissalinkert 'Tile performance improvements for VMS and NDPI' (label: exclude)
Already up-to-date.

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 999 melissalinkert 'Fix for single channel  meas_mode 13 data (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 1029 melissalinkert 'TIFF: adjust optimal tile height if tiles have height of 1 (rebased onto develop)'
  # PR 1030 melissalinkert 'CZI: restrict dimension adjustment (rebased onto develop)'
  # PR 1031 melissalinkert 'Volocity: parse timestamps from .atsf files (rebased onto develop)'
  # PR 1041 melissalinkert 'Minor docs autogen fixes (rebased onto develop)'
  # PR 1042 melissalinkert 'OME-XML package bug-fix (rebased onto develop)'
  # PR 1050 melissalinkert 'Add the series index to the default image name (rebased onto develop)'
  # PR 1053 melissalinkert 'SVS: store the PhysicalSizeX and PhysicalSizeY attributes'
  # PR 1056 rleigh-dundee 'Use ant to build sphinx docs'
  # PR 1057 melissalinkert 'Fix file handle/line ending issues so that tests pass on Windows'
  # PR 1058 rleigh-dundee 'source-archive: Close in use files before removing them'
Conflicting PRs (not included):
  # PR 1055 rleigh-dundee 'Fix up Bio-Formats POMs (rebased)'

Generated by OMERO-5.1-merge-push#168 (http://ci.openmicroscopy.org/job/OMERO-5.1-merge-push/168/)