Make compareRTypes more Ice-like

This converts the compareRTypes from using
raw pointers to Ice smart pointers.
Fix gtest assertions

GTest didn't like assertions of the form
`ASSERT_EQ(false, ...)`. Now using _TRUE
and _FALSE.
Fix rtype comparison using operators

The gt/lt comparisons were all failing in the
rtypes test. By defining the comparator operators,
(here for RString) these now pass.
Implement fixes from rleigh
Ensure user is in correct group for whole write.
Pass context.
Add comparison operators for other primitive types

Note: this breaks null proxy checks of the form
`x->getY() == 0`. Use `!x->getY()` instead.
Handle comparisons for RTypeSeq containers
Rename compareRTypeSeq to match compareRTypes
Merge pull request #2445 from ximenesuk/rebased/develop/bulk-annotations-12210

Fix permissions in bulk annotation script (rebased onto develop)
Merge pull request #2444 from joshmoore/cpp-utests

CPP unit test fixes
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 2258 will-moore 'Truncate js tree dynamically 12161' (user: will-moore)
  # PR 2256 will-moore 'Tablet drag handling' (user: will-moore)
  # PR 2435 rleigh-dundee 'cpp: RTypesI: use static locals in place of duplicated globals' (user: rleigh-dundee)
  # PR 2484 joshmoore 'Maven/ant improvements' (user: joshmoore)
  # PR 2362 will-moore 'Remove .jy from script names' (user: will-moore)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 2465 bpindelski 'Add missing deps to omero_client.jar (fix #12166) (rebased onto develop)' (user: bpindelski)
  # PR 2470 mtbc 'ensure that DB enum check is done only once per BF revision' (user: mtbc)
  # PR 2357 rleigh-dundee 'Generate Python API reference with Sphinx' (user: rleigh-dundee)
  # PR 2478 joshmoore '11479 Private Tags Bug (rebased onto develop)' (user: joshmoore)
  # PR 2455 rleigh-dundee 'Remove support for Ice 3.3' (user: rleigh-dundee)
  # PR 2127 dpwrussell 'Working view to email announcements to selected users, groups, email addresses and/or all users' (user: dpwrussell)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude)
  # PR 2428 ximenesuk 'Move kill session to global teardown' (user: ximenesuk)
  # PR 2486 joshmoore 'Fs cli plugin (rebased onto develop)' (user: joshmoore)
  # PR 2450 joshmoore 'Run session creation in system context' (user: joshmoore)
  # PR 2446 will-moore 'Enable multi-select in Tags tree' (user: will-moore)
  # PR 2403 aleksandra-tarkowska 'Send email' (user: aleksandra-tarkowska)
  # PR 2269 dominikl 'ROI improvements' (user: dominikl)
  # PR 2411 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 2336 knabar 'New tagging dialog' (user: knabar)
  # PR 2472 joshmoore 'Redirect parseInputs to getInputs (rebased onto develop)' (user: joshmoore)
  # PR 2481 joshmoore 'Servants per session (rebased onto develop)' (user: joshmoore)
  # PR 2391 jburel 'Imagej omero (rebased onto develop)' (user: jburel)
Already up-to-date.

Merged PRs:
  # PR 2412 qidane 'Extra annotations'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)' (user: melissalinkert)
  # PR 1082 rleigh-dundee 'C++: Add support for integers of different endianness' (user: rleigh-dundee)
  # 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 1060 melissalinkert 'Allow dist-matlab to run on Windows' (user: melissalinkert)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1092 sbesson 'Allow for a >1 count increment in B&H .sdt Files. (rebased onto develop)' (user: sbesson)
  # PR 981 melissalinkert 'Ignore namespaces when filling in an XMLAnnotation's Value' (user: melissalinkert)
  # PR 1049 melissalinkert 'DICOM: fix file grouping so that path names are normalized (rebased onto develop)' (user: melissalinkert)
  # PR 1070 melissalinkert 'DICOM: expand sequence reading to include known sequences (rebased onto develop)' (user: melissalinkert)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (user: melissalinkert)
  # PR 1028 melissalinkert 'Large fileset performance improvements (rebased onto develop)' (user: melissalinkert)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
Updating f247b30..d4ec8df
Merged PRs (fast-forward):
  # 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'

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

Repository: ome/scripts
Excluded PRs:
  # PR 79 sbesson 'Travis fix (rebased onto develop)' (user: sbesson)
  # 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 743 sbesson 'Propose redesign of OMERO and Bio-Formats 5.0 CI jobs' (exclude comment)
Updating be161c6..b156b28
Merged PRs (fast-forward):
  # 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'

Generated by OMERO-5.1-breaking-push#45 (http://ci.openmicroscopy.org/job/OMERO-5.1-breaking-push/45/)