add newly annotation entities to disk usage count

arising from https://github.com/openmicroscopy/openmicroscopy/pull/2412
include pyramid lock files in disk usage calculation
Add getter and setter methods for _event_context in CLI

Also fix the corresponding integration tests
Add getter and setter methods for _client in CLI
Add special handling for zero value in HqlControl.filter()

This commit should allow zero-values not to be filtered out when returning
the output of a query.
Add unit tests for HqlControl.filter()
Merge pull request #3110 from mtbc/trac-12552-disk-usage-for-extra-annotations

fix #12552: include extra annotations in disk usage calculation
Adjust integration test to new defaults
Merge pull request #3116 from sbesson/12572_hql_zerovalue

Handle zero value in CLI hql
Merge pull request #3114 from sbesson/12388_getter

CLI: add getter/setters for client/event context
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 3099 (DB 5.1__DEV11: unit support for time)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 3115 sbesson 'CLI admin diagnostics: only check readability of var folder' (user: sbesson)
  # PR 3119 bpindelski 'Remove the "dn" column from "password" (fix #2587).' (label: exclude)
  # PR 3118 ximenesuk 'Flake8 OmeroFS' (user: ximenesuk)
  # PR 3042 will-moore 'Download dataset project' (user: will-moore)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 3057 will-moore 'Rating web' (user: will-moore)
  # PR 3069 aleksandra-tarkowska 'Scalebar' (user: aleksandra-tarkowska)
  # PR 3117 dominikl 'Bugfix: Paste pending rendering settings' (user: dominikl)
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (exclude comment)
  # PR 3109 dpwrussell 'Disable keyboard navigation (up, down, left, right) for jquery tabs' (user: dpwrussell)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude)
  # PR 3120 sbesson 'Robot framework: add CLI plugin to generate configuration file' (user: sbesson)
  # PR 2985 will-moore 'Download preserves directories of original files' (user: will-moore)
  # PR 3037 joshmoore 'Group sudo' (user: joshmoore)
  # PR 3086 will-moore 'Create image by tiling 12459' (user: will-moore)
  # PR 3108 dominikl 'Fixed bug ChannelSlider (rendering settings)' (user: dominikl)
  # PR 3113 jburel 'Editor deprecation' (user: jburel)
  # PR 3000 jballanc 'Update artifacts for Lucene, Hibernate, and Spring' (user: jballanc)
  # PR 3098 aleksandra-tarkowska 'Metadata reimport' (user: aleksandra-tarkowska)
  # PR 3111 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 3058 sbesson 'Homebrew nginx (rebased onto develop)' (user: sbesson)
Already up-to-date.

Merged PRs:
  # PR 3099 joshmoore 'DB 5.1__DEV11: unit support for time'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1366 ctrueden 'Miscellaneous cleanup' (user: ctrueden)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (user: ctrueden)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1374 rleigh-dundee 'C++: Collected small fixes' (user: rleigh-dundee)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
Updating 5706a61..4fee2f2
Previously merged:
  # PR 1373 rleigh-dundee 'cpp: test: Only test multi_array assertions for release builds'
  # PR 1369 sbesson 'Document usage of setSeries() and getIndex() in MATLAB documentation'
  # PR 1371 rleigh-dundee 'C++: Read and write all pixel types and validate all tags and pixel data'
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories'
  # PR 1370 rleigh-dundee 'cpp: Adapt to Boost 1.56 optional changes'

Merged PRs:
  # PR 1265 qidane 'New units'
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient'

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

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 1014 bpindelski 'Ldap.txt: cleanup and update column names.' (user: bpindelski)
  # PR 990 kennethgillen 'for users who have compiled isapi_wsgi on x64' (user: kennethgillen)
Updating 99514d2..86c72bc
Previously merged:
  # PR 1013 snoopycrimecop 'Update auto-generated properties'
  # PR 1009 manics 'Update Linux walkthrough to 5.0.5 (rebased onto develop)'
  # PR 1012 sbesson 'Add documentation for new OME-help-release job'
  # PR 1011 sbesson 'Redirect Python API documentation to new Sphinx-generated pages'
  # PR 1010 hflynn 'Minor tidying of contributing docs'
  # PR 1008 hflynn 'Adding link to secvuln on sysadmin security page (rebased onto develop)'

Generated by OME-5.1-breaking-push#129 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/129/)