Merge pull request #2394 from joshmoore/rebased/develop/11990-loop-on-refs

Call updateObjects/updateReferences in a loop (rebased onto develop)
merge develop -D org: PR 2127 (Working view to email announcements to selected users, groups, email addresses and/or all users)
merge develop -D org: PR 2256 (Tablet drag handling)
merge develop -D org: PR 2258 (Truncate js tree dynamically 12161)
merge develop -D org: PR 2269 (ROI improvements)
merge develop -D org: PR 2357 (Generate Python API reference with Sphinx)
merge develop -D org: PR 2362 (Remove .jy from script names)
merge develop -D org: PR 2377 (OMERO.matlab: add utility function to load channels (rebased onto develop))
merge develop -D org: PR 2391 (Imagej omero (rebased onto develop))
merge develop -D org: PR 2401 (fix #12242: delete bad annotation links and annotations)
merge develop -D org: PR 2411 (Update develop submodules)
merge develop -D org: PR 2413 (Close ImportProcessPrx instances (Fix #12233) (rebased onto develop))
merge develop -D org: PR 2414 (Delete superfluous READMEs (rebased onto develop))
merge develop -D org: PR 2416 (remove TEST sql scripts (rebased from dev_5_0))
merge develop -D org: PR 2419 (Improve error message on missing lib/scripts (Fix #9785) (rebased onto develop))
merge develop -D org

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 2403 aleksandra-tarkowska 'Send email' (status: error)
  # PR 2412 qidane 'Extra annotations' (exclude comment)
  # PR 2336 knabar 'New tagging dialog' (exclude comment)
  # PR 2417 jburel 'Compression level (rebased onto develop)' (status: error)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude breaking)
  # PR 2182 joshmoore 'Read only flag' (label: exclude)
Already up-to-date.

Merged PRs:
  # PR 2127 dpwrussell 'Working view to email announcements to selected users, groups, email addresses and/or all users'
  # PR 2256 will-moore 'Tablet drag handling'
  # PR 2258 will-moore 'Truncate js tree dynamically 12161'
  # PR 2269 dominikl 'ROI improvements'
  # PR 2357 rleigh-dundee 'Generate Python API reference with Sphinx'
  # PR 2362 will-moore 'Remove .jy from script names'
  # PR 2367 dpwrussell 'Move webadmin navigation to base template'
  # PR 2377 sbesson 'OMERO.matlab: add utility function to load channels (rebased onto develop)'
  # PR 2391 jburel 'Imagej omero (rebased onto develop)'
  # PR 2401 mtbc 'fix #12242: delete bad annotation links and annotations'
  # PR 2411 snoopycrimecop 'Update develop submodules'
  # PR 2413 joshmoore 'Close ImportProcessPrx instances (Fix #12233) (rebased onto develop)'
  # PR 2414 hflynn 'Delete superfluous READMEs (rebased onto develop)'
  # PR 2416 mtbc 'remove TEST sql scripts (rebased from dev_5_0)'
  # PR 2419 joshmoore 'Improve error message on missing lib/scripts (Fix #9785) (rebased onto develop)'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 528 melissalinkert 'Tile performance improvements for VMS and NDPI' (label: exclude)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
Updating fd9b562..9d07147
Merged PRs (fast-forward):
  # PR 1075 hflynn 'Remove dead bitmap link (rebased onto develop)'
  # PR 1076 hflynn 'Adding CONTRIBUTING file to BF repo (rebased onto develop)'

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 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)'
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)'
  # PR 1060 melissalinkert 'Allow dist-matlab to run on Windows'
  # PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)'

Repository: ome/scripts
Already up-to-date.

Merged PRs:
  # PR 76 will-moore 'Fix 'No permissions' error in Make_Movie.py. See #12227'

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs' (exclude comment)
Updating be161c6..d5bcff5
Merged PRs (fast-forward):
  # PR 759 hflynn 'ticket 10030 fix - contributing file for docs repo (rebased onto develop)'
  # PR 761 rleigh-dundee 'Delegate all Makefile targets to ant'

Merged PRs:
  # PR 758 hflynn 'Adding API doc links to OMERO docs front page (rebased onto develop)'
  # PR 760 rleigh-dundee 'Make Ice 3.4 the minimum supported version'
  # PR 766 rleigh-dundee 'ant: Default all properties and handle empty vars in conf.py'

Generated by OMERO-5.1-merge-push#190 (http://ci.openmicroscopy.org/job/OMERO-5.1-merge-push/190/)