Revert commit f405abe - fix 'Save before Apply' bug reported in PR 1036
Improve description of graph loading in P/D/S get functions
Invert required arguments order in getObjects() for consistency

Fix all the getXXX() methods calling getObjects()
Fix hiding of single subset with multi-tags. PR #1054
Add hasOriginalMetadata so it is easier to handle on develop.
Remove getPlateAcquisitions() method

Since plate acquisition are always loaded when the plate is loaded, plate
acquisitions should be loaded with the getPlates() method.
merge dev_4_4 -D org -I include -E exclude: PR 821 (Connection)
merge dev_4_4 -D org -I include -E exclude: PR 988 (webgallery prototype from github/will-moore/webgallery)
merge dev_4_4 -D org -I include -E exclude: PR 1002 (Thumbnail figure)
merge dev_4_4 -D org -I include -E exclude: PR 1033 (Download image and metadata)
merge dev_4_4 -D org -I include -E exclude: PR 1036 (Copy paste rdefs 10673)
merge dev_4_4 -D org -I include -E exclude: PR 1045 (OMERO.matlab: add permissions to the object loading methods)
merge dev_4_4 -D org -I include -E exclude: PR 1050 (Import archived)
merge dev_4_4 -D org -I include -E exclude: PR 1053 (CLI: Improve user arguments allowing to specify input type)
merge dev_4_4 -D org -I include -E exclude: PR 1054 (Web bugs april17th)
merge dev_4_4 -D org -I include -E exclude

Repository: openmicroscopy/openmicroscopy
Already up-to-date.
Merged PRs:
  # PR 821 jburel 'Connection'
  # PR 988 will-moore 'webgallery prototype from github/will-moore/webgallery'
  # PR 1002 will-moore 'Thumbnail figure'
  # PR 1033 jburel 'Download image and metadata'
  # PR 1036 will-moore 'Copy paste rdefs 10673'
  # PR 1045 sbesson 'OMERO.matlab: add permissions to the object loading methods'
  # PR 1050 jburel 'Import archived'
  # PR 1053 sbesson 'CLI: Improve user arguments allowing to specify input type'
  # PR 1054 will-moore 'Web bugs april17th'

Repository: openmicroscopy/bioformats
Already up-to-date.
Merged PRs:
  # PR 379 sbesson 'Fix source code links moved to the scifio-tools foder'

Repository: ome/scripts
Already up-to-date.
Merged PRs:
  # PR 27 will-moore 'Group thumbs by tag (only show each thumb once)'

Repository: openmicroscopy/ome-documentation
Already up-to-date.
Merged PRs:
  # PR 281 sbesson 'Review Matlab documentation (see #10389)'
  # PR 334 sbesson 'Add GH/Jenkins extlinks to the model documentation'

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