IFormatReader: Remove deprecated getChannelDimLengths and getChannelDimTypes

The only reader overriding the default implementations was ICSReader.
This has been updated to use ModuloC, which copes with the case
where all channels are of the same length.

The users of these methods (plugins DisplayHandler, ImagePlusReader,
LociFunctions and BFVirtualStack) have been updated to make use of
ModuloC.

These methods have been dropped from all implementors of IFormatReader.
IFormatReader: Remove deprecated getCoreMetadata
Convert tolerance to NonNegativeInt to NonNegativeFloat
Ordered MapPairs implementation

After feedback from the client developers, the contents
of the MapPairs class which was previously a string-string
map has been converted into a list of string-string pairs.

The `getMap()` method is now `getPairs()` and where possible
mutation of the contents is prevented, e.g. by making the
fields of MapPair immutable and using copy-constructors
rather than setters where possible.

Still slightly unclear is if the naming of the "map" is
correct now that it's no longer based on a hash map, and
whether the value of the MapPair will ever need to be anything
other than a string.
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1418 (IFormatReader: Remove deprecated methods)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1425 (Convert tolerance to NonNegativeInt to NonNegativeFloat)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1435 (Ordered MapPairs implementation)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1430 sbesson 'Matlab units metadata' (user: sbesson)
  # PR 1407 melissalinkert 'TIFF: fix plane count calculation for pyramids with multiple planes' (user: melissalinkert)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (user: ctrueden)
  # PR 1420 qidane 'Updating samples and adding units samples' (user: qidane)
  # PR 1421 jburel 'Units mock' (user: jburel)
  # PR 1426 qidane 'Initial Rendering Definitions schema' (exclude comment)
  # PR 1431 rleigh-dundee 'Specification: Add XML catalogues for released schemas' (user: rleigh-dundee)
  # PR 1383 LeeKamentsky 'Fix im3 metadata' (user: LeeKamentsky)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # 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 1428 rleigh-dundee 'C++: Incremental metadata processing work' (user: rleigh-dundee)
  # PR 1423 melissalinkert 'TIFF: attempt to correct incorrectly stored StripByteCounts values' (user: melissalinkert)
  # PR 1433 melissalinkert 'Initial version of I2I reader' (user: melissalinkert)
  # 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 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1434 rleigh-dundee 'cpp: cmake: RegexChecks: Improve include usage for portability' (user: rleigh-dundee)
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient' (user: melissalinkert)
  # PR 1422 melissalinkert 'Zeiss TIFF: fix used file list when expected files are missing' (user: melissalinkert)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1432 melissalinkert 'Metamorph: fix description delimiter to account for XML sanitization' (user: melissalinkert)
Updating e88645d..80e0ffe
Previously merged:
  # PR 1427 rleigh-dundee 'C++: Path handling and installation location introspection'
  # PR 1429 qidane 'Change working distance back to UNITS.MICROM'
  # PR 1419 sbesson 'Flake8 Bio-Formats Python files'
  # PR 1424 melissalinkert 'DICOM: fix dimension population for multi-series filesets'
  # PR 1385 rleigh-dundee 'C++: Add TIFF reader'

Merged PRs:
  # PR 1418 rleigh-dundee 'IFormatReader: Remove deprecated methods'
  # PR 1425 jburel 'Convert tolerance to NonNegativeInt to NonNegativeFloat'
  # PR 1435 joshmoore 'Ordered MapPairs implementation'

Generated by OME-5.1-breaking-push#202 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/202/)