Set default socket timeout correctly (Fixes #12097)

Python socket timeouts are specified in seconds as floating point.  This
commit sets the default timeout to a more reasonable 3 seconds, allows
the specification of a floating point timeout value, removes the
assumption that the timeout is specified in milliseconds and documents
all of the aforementioned.
Support for configuring the upgrade check URL (See #12097)

This commit adds configurability to the upgrade check URL via the
OMERO.web configuration mechanism.  Upgrade checks in OMERO.web can now
be disabled by running:

    bin/omero config set omero.web.upgrades_url ''
Use existing "omero.upgrades.url" configuration option
Add Trusted-Only:true to the Insight manifest.

See http://docs.oracle.com/javase/6/docs/technotes/guides/jweb/mixed_code.html#trusted_only
Don't sign the webstart jars by default.

We're going to be code-signing in a separate process, so this prevents jars being double-signed, once with the self-signed cert and once with a proper one.

The webstart-sign target is still there, so you can use `./build.py webstart-sign release-webstart`.
remove import logs as annotations on other entities
fix 11965: join images to plate runs for leaf queries
Add an external webstart signing script

Automatically run this script with the existing self-signed certificate as part of the standard docs/hudson/OMERO.sh build
Merge pull request #2176 from chris-allan/12097-socket-timeout

dev_5_0: Update upgrade check handling in OMERO.web
Merge pull request #2203 from mtbc/import-log-sql-fix

remove import logs as annotations on other entities (merging for `5.0.1`)
Merge pull request #2221 from mtbc/trac-11965-plate-join-image-leaves

fix #11965: join images to plate runs for leaf queries (merging for `5.0.1`)
Merge pull request #2193 from manics/more_webstart_codesigning_tweaks

More webstart code-signing changes (merging for `5.0.1`)
Update dev_5_0 submodules

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

Repository: openmicroscopy/bioformats
Updating 85f8d80..f336f17
Merged PRs (fast-forward):
  # PR 1017 melissalinkert 'Add missing jgoodies-common dependency'
  # PR 1011 joshmoore 'ITK documentation fixes from @iMichka'
  # PR 951 ctrueden 'Fix up Bio-Formats POMs'
  # PR 1009 melissalinkert 'TIFF: adjust optimal tile height if tiles have height of 1'
  # PR 987 melissalinkert 'Volocity: parse timestamps from .atsf files'
  # PR 1003 melissalinkert 'Large fileset performance improvements'
  # PR 972 melissalinkert 'CZI: restrict dimension adjustment'
  # PR 1000 melissalinkert 'Metadata fixes'
  # PR 989 melissalinkert 'ND2: always set the field index to 2'
  # PR 997 melissalinkert 'Make macro recording work with Exporter (rebased onto dev_5_0)'
  # PR 993 bpindelski 'Update docs regarding BF and Eclipse (see #12127).'
  # PR 984 melissalinkert 'Enable SDT plane preloading by default'
  # PR 979 melissalinkert 'SVS import and TIFF export fixes'
  # PR 915 imunro 'Fix for single channel  meas_mode 13 data.'
  # PR 988 melissalinkert 'InCell: fix NPE when parsing Z positions'
  # PR 960 melissalinkert 'Cache OME-XML between ImagePluses (rebased onto dev_5_0)'
  # PR 952 melissalinkert 'Memoization fixes'
  # PR 946 melissalinkert 'Read internal pyramids from CellSens .vsi data'
  # PR 968 melissalinkert 'Cellomics: a few fixes for single-file datasets (rebased onto dev_5_0)'
  # PR 957 melissalinkert 'Correctly set Modulo annotations for multi-Image datasets (rebased onto dev_5_0)'
  # PR 958 melissalinkert 'Flex: be more permissive in parsing IFDs and XML (rebased onto dev_5_0)'
  # PR 976 hflynn 'Fix links to Zeiss image browser software'
  # PR 941 melissalinkert 'Fix the download URL for stable release jars'
  # PR 969 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes'

Repository: ome/scripts
Updating c0916f6..6cc0a0b
Merged PRs (fast-forward):
  # PR 72 sbesson 'Fix scripts to comply with PEP8 1.5.0'
  # PR 68 will-moore 'Kymograph_Analysis creates single csv. See #11909 (rebased onto dev_5_0)'

Repository: openmicroscopy/ome-documentation
Updating 85c8eab..846e636
Merged PRs (fast-forward):
  # PR 712 rleigh-dundee 'Unix/Linux installation: Update requirements'
  # PR 710 manics 'Update supported Linux versions for 5.0'
  # PR 711 hflynn 'Homebrew install edits (rebased onto dev_5_0)'
  # PR 703 hflynn 'Updates to sysadmin installation docs'
  # PR 705 sbesson 'Move schema changes to the contributing documentation (rebased onto dev_5_0)'
  # PR 702 bpindelski 'Remove paragraph about whitespace and Ice. (rebased onto dev_5_0)'
  # PR 698 joshmoore 'Fix Windows paths error found by Javier Colmeiro'
  # PR 696 hflynn 'Removing contributing & formats docs from dev_5_0'

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