Only use ReferenceList for true references

In particular, it should not be used when attaching Images etc. to the
OME object.
Merge pull request #1474 from sbesson/rebased/develop/rebased/dev_5_0/copyright_tools

Add bash script for updating copyright headers (rebased onto dev_5_0) (rebased onto develop)
cpp: xerces: Generalise document writing to all nodes
Merge pull request #1472 from rleigh-dundee/cpp-compat-bool

cpp: compat: Add boolean type
Merge pull request #1473 from rleigh-dundee/cpp-array-docfix

C++: Minor documentation and whitespace fixes
Merge pull request #1471 from jburel/mock-sample

mock object
Merge pull request #1458 from sbesson/javadocs_warnings

Fix Javadocs warnings
cpp: bioformats: Add resolve argument to resolveReferences
cpp: compat: Add C++98/boost std::owner_less fallback

The following implementations are supported:

- C++11 std::owner_less
- Boost boost::owner_less (newer Boost versions aligned with C++11)
- Our fallback reimplementation (older Boost versions)
xsd-fu: Use multi-index for C++ reference lists

boost::multi_index_container is used to index elements by both
index number (insertion order) and value (pointer location).
This allows access by index and fast lookup without the need
for an O(n) list traversal.

This is similar to the Java ReferenceList but does not implement
a container in its own right; it's just a specialisation of an
existing multi-indexing container implementation as a typedef.
The code generator has been updated to emit the new container
types in place of std::vector, and the C++ code templates
adjusted to use them for fast lookups.
merge develop -Dorg -Ssuccess-only: PR 1407 (TIFF: fix plane count calculation for pyramids with multiple planes)
merge develop -Dorg -Ssuccess-only: PR 1442 (Update roi handler)
merge develop -Dorg -Ssuccess-only: PR 1461 (Changed ND2 metadata string handling to work properly with empty strings)
merge develop -Dorg -Ssuccess-only: PR 1477 (Flex: improved metadata handling)
merge develop -Dorg -Ssuccess-only: PR 1478 (C++: Add helpers for XML serialisation)
merge develop -Dorg -Ssuccess-only: PR 1481 (cpp: bioformats: Add resolve argument to resolveReferences)
merge develop -Dorg -Ssuccess-only: PR 1482 (xsd-fu: Use multi-index for C++ reference lists)
merge develop -Dorg -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1480 melissalinkert 'Imspector OBF: support version 5 stacks' (status: failure)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (label: exclude)
  # PR 1479 qidane 'Updated XSLT for units conversion' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1426 qidane 'Initial Rendering Definitions schema' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1483 sbesson 'Update copyright: add support for unicode' (status: pending)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1443 joshmoore 'Genshi ZIP' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
Already up-to-date.

Merged PRs:
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes'
  # PR 1442 bramalingam 'Update roi handler'
  # PR 1461 csachs 'Changed ND2 metadata string handling to work properly with empty strings'
  # PR 1477 melissalinkert 'Flex: improved metadata handling'
  # PR 1478 rleigh-dundee 'C++: Add helpers for XML serialisation'
  # PR 1481 rleigh-dundee 'cpp: bioformats: Add resolve argument to resolveReferences'
  # PR 1482 rleigh-dundee 'xsd-fu: Use multi-index for C++ reference lists'

Generated by OME-5.1-merge-push#643 (http://ci.openmicroscopy.org/job/OME-5.1-merge-push/643/)