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

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)
Updating f8a8707..f1dbd98
Merged PRs (fast-forward):
  # PR 1047 sbesson 'Update auto-generated documentation'
  # PR 1040 melissalinkert 'Only add a MetadataOnly element if no TiffData elements are present (rebased onto dev_5_0)'
  # PR 1033 melissalinkert 'Add the series index to the default image name'
  # PR 1024 melissalinkert 'DICOM: fix file grouping so that path names are normalized'

Merged PRs:
  # PR 998 melissalinkert 'Micromanager fixes'
  # PR 1018 melissalinkert 'Flex: fix support for new file naming scheme'

Generated by OMERO-5.0-merge-daily#630 (http://ci.openmicroscopy.org/job/OMERO-5.0-merge-daily/630/)