Merge pull request #1024 from melissalinkert/dicom-file-grouping

DICOM: fix file grouping so that path names are normalized
Merge pull request #1033 from melissalinkert/sdt-image-name

Add the series index to the default image name
Merge pull request #1040 from melissalinkert/rebased/dev_5_0/metadataonly

Only add a MetadataOnly element if no TiffData elements are present (rebased onto dev_5_0)
Merge pull request #1047 from snoopycrimecop/autogen/dev_5_0/latest

Update auto-generated documentation
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)
Already up-to-date.

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

Generated by BIOFORMATS-5.0-merge-daily#793 (http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-merge-daily/793/)