Add integration test for CLI import as functionality
Refactor sudo_args and add failing test for multi-group CLI import as
Mark multi-group import as test as xfail
Add failing to test for regular import in multi-group
Keep smart folders when sorting. (see #12294)
Remove commented code and comments

No longer required.
Make sure the smart folder is always at the bottom.
Merge pull request #2588 from sbesson/rebased/develop/cli_importsudo

Add integration tests for CLI import as (rebased onto develop)
Merge pull request #2598 from jburel/rebased/develop/orphaned-missing

Orphaned missing (rebased onto develop)
Update develop submodules

Repository: openmicroscopy/openmicroscopy
Already up-to-date.

Repository: openmicroscopy/bioformats
Updating f247b30..73a2cea
Merged PRs (fast-forward):
  # PR 1158 hflynn 'Removing dead link from Minolta-MRW format page (rebased onto develop)'
  # PR 1110 sbesson 'BF docs: Jenkins cleanup (rebased onto develop)'
  # PR 1147 rleigh-dundee 'cpp: bioformats: PixelProperties supports pixel types of different endianness'
  # PR 1152 hflynn 'Comstat2 link (rebased onto develop)'
  # PR 1149 sbesson 'Add prefix to zip file produced by dist-bftools target (rebased onto develop)'
  # PR 1106 melissalinkert 'Imaris HDF: make sure that all resolutions have the same ZCT sizes (rebased onto develop)'
  # PR 1097 melissalinkert 'CellSens: fix off-by-ones in subresolution tile calculations (rebased onto develop)'
  # PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)'
  # PR 1060 melissalinkert 'Allow dist-matlab to run on Windows'
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)'
  # PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)'
  # PR 1135 joshmoore 'Update native-lib-loader to 2.0.1 release (rebased onto develop)'
  # PR 1142 hflynn 'Add 'show and edit on Github' to docs side menu (rebased onto develop)'
  # PR 1137 melissalinkert 'Update version history for 5.0.2 (rebased onto develop)'
  # PR 1103 melissalinkert 'Flex: fix support for new file naming scheme (rebased onto develop)'
  # PR 1092 sbesson 'Allow for a >1 count increment in B&H .sdt Files. (rebased onto develop)'
  # PR 1101 melissalinkert 'QuickTime: fix header/footer parsing bug (rebased onto develop)'
  # PR 1127 sbesson 'CI logging improvements (rebased onto develop)'
  # PR 1102 melissalinkert 'Metamorph .nd performance improvements (rebased onto develop)'
  # PR 1109 melissalinkert 'Fix memo file path creation on Windows (rebased onto develop)'
  # PR 1100 melissalinkert 'Fix single plane ND2 line scan (rebased onto develop)'
  # PR 1096 melissalinkert 'Fix 5D Imspector support (rebased onto develop)'
  # PR 1098 melissalinkert 'Gatan metadata fixes (rebased onto develop)'
  # PR 1082 rleigh-dundee 'C++: Add support for integers of different endianness'
  # PR 1120 rleigh-dundee 'cpp: ome-bioformats: Use std::complex for complex pixel types'
  # PR 1118 joshmoore 'LogbackTools: silence ClassCastException traces (rebased onto develop)'
  # PR 1128 hflynn 'Update auto-generated documentation on develop'
  # PR 1119 hflynn 'User docs tidying (rebased onto develop)'
  # PR 1099 melissalinkert 'Disable file grouping in ImageJ remote import plugin (rebased onto develop)'
  # PR 1107 melissalinkert 'Exclude log4j and packages from target-test-runner (rebased onto develop)'
  # PR 1121 sbesson 'Fix bfGetPlane tile input check (rebased onto develop)'
  # PR 1117 rleigh-dundee 'cpp: Minor doxygen fixes'
  # PR 1126 hflynn 'Leica link (rebased onto develop)'
  # PR 1083 rleigh-dundee 'make: Convert variables to ant properties'
  # 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'

Repository: ome/scripts
Updating 31f89c4..491d96e
Merged PRs (fast-forward):
  # PR 76 will-moore 'Fix 'No permissions' error in Make_Movie.py. See #12227'
  # PR 81 will-moore 'Make movie format time 12254 (rebased onto develop)'
  # PR 84 sbesson 'Get inputs all scripts (rebased onto develop)'
  # PR 79 sbesson 'Travis fix (rebased onto develop)'

Repository: openmicroscopy/ome-documentation
Updating be161c6..6e003c4
Merged PRs (fast-forward):
  # PR 817 ximenesuk 'Update DropBox documentation (rebased onto develop)'
  # PR 812 sbesson 'Remaining changes post 5.0.x job migration'
  # PR 816 will-moore 'Webgateway mip 5150 (rebased onto develop)'
  # PR 814 bpindelski 'Add LDAP error message explanation.'
  # PR 806 aleksandra-tarkowska 'Webstart template (rebased onto develop)'
  # PR 807 aleksandra-tarkowska 'ldap over ssl instruction improvement (rebased onto develop)'
  # PR 805 hflynn 'Adding contributing doc link & Zeiss link update'
  # PR 810 hflynn 'Adding example server setup page  (rebased onto develop)'
  # PR 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs'
  # PR 809 sbesson 'Travis fix (rebased onto develop)'
  # PR 802 snoopycrimecop 'Update index.txt'
  # PR 801 sbesson 'Add Edit on Github button (rebased onto develop)'
  # PR 783 mtbc 'document new // separator in omero.fs.repo.path (rebased from dev_5_0)'
  # PR 782 will-moore 'Custom web login 11961 (rebased onto develop)'
  # PR 795 manics 'Root password reset command (rebased onto develop)'
  # PR 786 mtbc 'warn that in-place ln_s can be slower for HCS (rebased from dev_5_0)'
  # PR 797 ximenesuk 'Add DropBox Windows requirements'
  # PR 793 hflynn 'Ice35 support for Windows (rebased to develop)'
  # PR 791 hflynn 'Limitations update for 5.0.2 (rebased onto develop)'
  # PR 792 bpindelski 'Remove repetition of the word "files" (rebased onto develop)'
  # PR 787 manics 'Add code-signing documentation (rebased onto develop)'
  # PR 776 sbesson 'Remove all references to CI jobs in the official documentation'
  # PR 772 rleigh-dundee 'make: Convert variables to ant properties'
  # 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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