source-archive: Close in use files before removing them

Required for Windows.
merge dev_5_0 -D org: PR 998 (Micromanager fixes)
merge dev_5_0 -D org: PR 1018 (Flex: fix support for new file naming scheme)
merge dev_5_0 -D org: PR 1059 (source-archive: Close in use files before removing them (rebased))
merge dev_5_0 -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1045 imunro 'Changes to ensure pmtMarker is read correctly.' (label: exclude)
  # PR 1016 ctrueden 'Use pom-scijava as parent' (label: exclude)
Already up-to-date.

Merged PRs:
  # PR 998 melissalinkert 'Micromanager fixes'
  # PR 1018 melissalinkert 'Flex: fix support for new file naming scheme'
  # PR 1059 rleigh-dundee 'source-archive: Close in use files before removing them (rebased)'

Generated by BIOFORMATS-5.0-merge-daily#801 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-merge-daily/801/)