adjust annotation link handling in graph traversal
fix some references to obsolete annotations
Merge pull request #5 from mtbc/extra-annotations-qidane

graph traversal and test fixes
Adding OMEROMetadataStore functions for new Refs
merge develop -D none -I breaking -E exclude: PR 2412 (Extra annotations)
merge develop -D none -I breaking -E exclude

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 2471 jburel 'Cut menu tb (rebased onto develop)' (user: jburel)
  # PR 2430 will-moore 'Allow 'Cut' instead of 'Copy' when orphaned Dataset selected' (user: will-moore)
  # PR 2470 mtbc 'ensure that DB enum check is done only once per BF revision' (user: mtbc)
  # PR 2459 mtbc 'remove obsolete dropbox directory check' (user: mtbc)
  # PR 2445 ximenesuk 'Fix permissions in bulk annotation script (rebased onto develop)' (user: ximenesuk)
  # PR 2391 jburel 'Imagej omero (rebased onto develop)' (user: jburel)
  # PR 2467 carandraug 'omero.scripts.Type: add getter for name attr.' (user: carandraug)
  # PR 2444 joshmoore 'CPP unit test fixes' (user: joshmoore)
  # PR 2465 bpindelski 'Add missing deps to omero_client.jar (fix #12166) (rebased onto develop)' (user: bpindelski)
  # PR 2446 will-moore 'Enable multi-select in Tags tree' (user: will-moore)
  # PR 2336 knabar 'New tagging dialog' (user: knabar)
  # PR 2256 will-moore 'Tablet drag handling' (user: will-moore)
  # PR 2258 will-moore 'Truncate js tree dynamically 12161' (user: will-moore)
  # PR 2455 rleigh-dundee 'Remove support for Ice 3.3' (user: rleigh-dundee)
  # PR 2357 rleigh-dundee 'Generate Python API reference with Sphinx' (user: rleigh-dundee)
  # PR 2367 dpwrussell 'Move webadmin navigation to base template' (user: dpwrussell)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 2426 dominikl 'Bugfix: Prevent user/group deletion' (user: dominikl)
  # PR 2450 joshmoore 'Run session creation in system context' (user: joshmoore)
  # PR 2362 will-moore 'Remove .jy from script names' (user: will-moore)
  # PR 2269 dominikl 'ROI improvements' (user: dominikl)
  # PR 2411 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 2403 aleksandra-tarkowska 'Send email' (user: aleksandra-tarkowska)
  # PR 2428 ximenesuk 'Move kill session to global teardown' (user: ximenesuk)
  # PR 2127 dpwrussell 'Working view to email announcements to selected users, groups, email addresses and/or all users' (user: dpwrussell)
  # PR 2435 rleigh-dundee 'cpp: RTypesI: use static locals in place of duplicated globals' (user: rleigh-dundee)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude)
Already up-to-date.

Merged PRs:
  # PR 2412 qidane 'Extra annotations'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 1082 rleigh-dundee 'C++: Add support for integers of different endianness' (user: rleigh-dundee)
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)' (user: melissalinkert)
  # PR 528 melissalinkert 'Tile performance improvements for VMS and NDPI' (user: melissalinkert)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)' (user: melissalinkert)
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value' (user: melissalinkert)
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)' (user: melissalinkert)
  # PR 1083 rleigh-dundee 'make: Convert variables to ant properties' (user: rleigh-dundee)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1060 melissalinkert 'Allow dist-matlab to run on Windows' (user: melissalinkert)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)' (user: melissalinkert)
Updating f247b30..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)'
  # PR 1073 rleigh-dundee 'docs: Delegate all sphinx Makefile targets to ant'

Merged PRs:
  # PR 1054 qidane 'Additional annotation points throughout the model'

Repository: ome/scripts
Excluded PRs:
  # PR 76 will-moore 'Fix 'No permissions' error in Make_Movie.py. See #12227' (user: will-moore)
Already up-to-date.

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 776 sbesson 'Remove all references to CI jobs in the official documentation' (user: sbesson)
  # PR 772 rleigh-dundee 'make: Convert variables to ant properties' (user: rleigh-dundee)
  # PR 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs' (exclude comment)
Updating be161c6..309d0cf
Merged PRs (fast-forward):
  # PR 771 hflynn 'Adding pyramid generation data duplication warning to in-place import (rebased onto develop)'
  # PR 760 rleigh-dundee 'Make Ice 3.4 the minimum supported version'
  # PR 768 hflynn 'Rephrasing CONTRIBUTING re: branch for PRs (rebased onto develop)'
  # PR 769 hflynn 'Making API doc links point at release version (rebased onto develop)'
  # PR 766 rleigh-dundee 'ant: Default all properties and handle empty vars in conf.py'
  # PR 758 hflynn 'Adding API doc links to OMERO docs front page (rebased onto develop)'
  # PR 759 hflynn 'ticket 10030 fix - contributing file for docs repo (rebased onto develop)'
  # PR 761 rleigh-dundee 'Delegate all Makefile targets to ant'

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