Upgrade to Hibernate 3.6 (See #2570)
Update Lucene to v3.1.0

This diff updates OMERO from Lucene v2.4.1 to v3.1.0. The most recent
stable version of Lucene (as of this commit) is v4.9.0, however v4.7.2
is that last version to still support Java 6 and v3.6.2 is the latest
version still supported by Hibernate-Search. If/when OMERO drops
support for Java 6, and after Hibernate-Search v5 reaches general
release, we should update Lucene again.

Note by Josh Moore: Using 3.1.0 in order to match Hibernate
                    3.6.10.Final

Aside from updating the library version, the following additional
changes were required for the server to compile:

* Renamed a few imports that were relocated
* Updated `CharTokenizer` subclass to handle `int`s instead of `char`s
* Changed `FullTextAnalyzer` to use updated `createComponents` API
* Added back-compat arguments (`LUCENE_30`) to a few constructors (note:
  this enum name has changed in v4.9.0 to `LUCENE_3_0`)
* Rewrote `SimilarTerms#do` method to use new `FuzzyTermsEnum` technique

Note: With this commit the server and client will build, but will not
run. The reason for this is that the version of Hibernate Search we
build with uses the old strategy for subclassing `Analyzer`.

Conflicts:
	build.xml
	etc/omero.properties
Revert Hibernate 4 changes
Fix package names and method signatures for tests

This change replicates the previous changes made to update package
names, remove the SqlException signature for `HibernateCallback`, and
add the Lucene version constants in some of the tests.

Note by Josh Moore: only taking Lucene test changes
Update TokenizationTest for new TokenStream API

The `TokenStream` in Lucene no longer operates like a vanilla iterator
with `next()`. Instead we need to retrieve the `Token` using the
`getAttributes()` method and advance the stream using the
`incrementToken()` method.
Revert "Update TokenizationTest for new TokenStream API"

This reverts commit de5c9bbed27da342b8882dbe4140f5988a19a4ff.
Rollback to hibernate search 3.3
Revert FullTextAnalyzer changes
Revert "Revert "Update TokenizationTest for new TokenStream API""

This reverts commit 9c4adf943ec66d42b9f20eb0726eba4a6f79ce19.
Bump Spring version to 3.1.4
Fix Spring and Hibernate dependencies
Bump JDBC driver as well (9.3-1102-jdbc4)
Fix TokenizationTest
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 3181 (Update to Hibernate 3.6 (See trac2570))
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/openmicroscopy
Excluded PRs:
  # PR 2585 aleksandra-tarkowska 'making time_zone and first_day_of_week configurable' (exclude comment)
  # PR 3156 aleksandra-tarkowska 'Templates cleanup' (user: aleksandra-tarkowska)
  # PR 3037 joshmoore 'Group sudo' (user: joshmoore)
  # PR 3175 will-moore 'General pane web' (user: will-moore)
  # PR 3184 jburel 'Roi lsm' (user: jburel)
  # PR 3069 aleksandra-tarkowska 'Scalebar' (user: aleksandra-tarkowska)
  # PR 3000 jballanc 'Update artifacts for Lucene, Hibernate, and Spring' (user: jballanc)
  # PR 3148 jburel 'Rnd rgb' (user: jburel)
  # PR 3086 will-moore 'Create image by tiling 12459' (user: will-moore)
  # PR 3133 dominikl 'General Pane alignment' (user: dominikl)
  # PR 3160 ximenesuk 'Try search repeatedly until success' (user: ximenesuk)
  # PR 3115 sbesson 'CLI admin diagnostics: only check readability of var folder' (user: sbesson)
  # PR 3146 joshmoore 'Add Length unit & update code' (user: joshmoore)
  # PR 3127 will-moore 'Batch Annotate with Read-only' (user: will-moore)
  # PR 3167 snoopycrimecop 'Update develop submodules' (user: snoopycrimecop)
  # PR 3183 bpindelski 'Add DN for groups (fix #6719).' (exclude comment)
  # PR 3142 jburel 'Deprecate  methods/services' (user: jburel)
  # PR 2182 joshmoore 'Read only flag' (user: joshmoore)
  # PR 3157 jburel 'Reset password' (user: jburel)
  # PR 2363 dominikl 'Java Gateway API' (label: exclude)
  # PR 3155 jburel 'Re changes' (user: jburel)
  # PR 3098 aleksandra-tarkowska 'Metadata reimport' (user: aleksandra-tarkowska)
  # PR 3058 sbesson 'Homebrew nginx (rebased onto develop)' (user: sbesson)
  # PR 3109 dpwrussell 'Disable keyboard navigation (up, down, left, right) for jquery tabs' (user: dpwrussell)
  # PR 3174 dominikl 'Distorted 'Send feedback' dialog' (user: dominikl)
  # PR 3042 will-moore 'Download dataset project' (user: will-moore)
  # PR 3176 dominikl 'Edit DoubleAnnotations' (user: dominikl)
Already up-to-date.

Merged PRs:
  # PR 3181 joshmoore 'Update to Hibernate 3.6 (See trac2570)'
Conflicting PRs (not included):
  # PR 3141 dpwrussell 'jstree upgrade (Functionality Review Only)'

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1383 LeeKamentsky 'Fix im3 metadata' (user: LeeKamentsky)
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes' (user: melissalinkert)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1385 rleigh-dundee 'C++: Add TIFF reader' (user: rleigh-dundee)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (user: melissalinkert)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1417 joshmoore 'Units length' (user: joshmoore)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (user: ctrueden)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (user: ctrueden)
Updating e9cb435..664309e
Previously merged:
  # PR 1415 melissalinkert 'Update Travis to build the 'utils' Ant target'
  # PR 1395 rleigh-dundee 'C++: Various minor fixes'
  # PR 1413 rleigh-dundee 'C++: Correct version embedding'
  # PR 1416 melissalinkert 'Update version history for 5.0.6 (rebased onto develop)'
  # PR 1404 melissalinkert 'Re-enable URLHandleTest'
  # PR 1411 melissalinkert 'Metamorph: fix double value parsing for locales that use a comma separator'
  # PR 1412 melissalinkert 'Zeiss CZI: prepend 0s so that image names are all the same length'
  # PR 1410 mtbc 'add RandomAccessOutputStream(byte[]) constructor'
  # PR 1409 hflynn 'Removing jpeg 2000 broken link (rebased onto develop)'
  # PR 1403 hflynn 'Removing dead visiquest link'
  # PR 1387 sbesson 'Fix testng JAR for Bio-Formats tools components'
  # PR 1384 melissalinkert 'OME-TIFF: return blank planes if the corresponding file does not exist'
  # PR 1386 melissalinkert 'Zeiss CZI: fix dimension calculations when expected planes are missing'
  # PR 1397 hflynn 'replacing boostpro link'

Merged PRs:
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient'

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

Repository: openmicroscopy/ome-documentation
Excluded PRs:
  # PR 990 kennethgillen 'for users who have compiled isapi_wsgi on x64' (user: kennethgillen)
Updating d7681c9..436c249
Previously merged:
  # PR 1027 hflynn 'Adding note about openjdk8 not being supported (rebased onto develop)'
  # PR 1014 bpindelski 'Ldap.txt: cleanup and update column names.'
  # PR 1022 hflynn 'In-place import user & group set-up plus minor tidy'
  # PR 1021 sbesson 'Review documentation for release infrastructure'
  # PR 1024 hflynn 'Variable names in example are swapped (rebased onto develop)'

Generated by OME-5.1-breaking-push#184 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/184/)