Remove legacy ome-editor and ome-notes
FormatReader: Add setCoreIndex, toSeries and toCoreIndex

setSeries and getSeries work by using coreIndex to compute the correct
value (replaces series), while getCoreIndex and setCoreIndex use the
coreIndex directly.  Readers using series directly have been fixed to
use getSeries.

toSeries and toCoreIndex methods convert between series and core index
numbers, and handle resolution flattening.  All functions dealing with
series numbering use these to handle conversion.
LeicaSCNReader: Handle 2010/10/01 schema

Allow use of both the
  http://www.leica-microsystems.com/scn/2010/03/10 and
  http://www.leica-microsystems.com/scn/2010/10/01
schemas.

- In order to handle both schemas identically, the pixels element
  sizeR/sizeZ/sizeC/firstIFD attributes are no longer parsed; instead
  the sizes for R, Z and C are computed from the dimensions elements.
  We do require that the dimensions are a non-sparse array.
- Fix data order as XYCZT (this matches the existing test cases).
- Thumbnails:
  + Correct IFD mapping for thumbnails
  + Get thumbnail size from correct image
  + Use flattened resolutions when getting thumbnails
LeicaSCNReader: Work with any schema version

Warn if the schema is unsupported, but otherwise try to read it.
Add setCoreIndex to DelegateReader and FileStitcher

This required adding toSeries and toCoreIndex to IFormatReader
(and hence ImageReader).
Rename toSeries to coreIndexToSeries and toCoreIndex to seriesToCoreIndex
FileStitcher: Don't use subresolutions conversions

Subresolutions are not supported.  This removes the need for
series ↔ coreIndex conversion, since they are always the same.
FileStitcher: Add seriesToCoreIndex and coreIndexToSeries methods

These override the ReaderWrapper implementation, and return their
argument (since subresolutions are not supported).
FileStitcher: Delegate seriesToCoreIndex and coreIndexToSeries to reader
LeicaSCNReader: Use LOGGER rather than System.out
LeicaSCNReader: Remove unused commented definition
FormatReader: Maintain series in addition to coreIndex

This enables getSeries to be O(1) in addition to coreIndex.
seriesToCoreIndex and coreIndexToSeries are also O(1) when
the current series/coreIndex matches their arguments.

FileStitcher also has a series member, but this is currently
unused; it was added purely to match the FormatReader behaviour.
Cellomics: set well count to 1 if only one file is found

See #9780.
Amira: make sure that the buffer is cleared between reads

See #9773.
AVI: be sure to reset the file pointer

See #9775.
Fixed number conversion in ITKBridgePipes

ITKBridgePipes was parsing several doubles as integers. These are now
appropriately parsed using Double.parseDouble().
ITKBridgePipes: Test for null when closing

ITKBridgePipes maintains both a reader and a writer. It now checks each
before closing both, in case only one is currently in use, to avoid a
NPE.
itkBFImageIO uses ITK API properly

When accessing region or ImageIO information, instead of directly
accessing the data structures (via m_XXX access) the appropriate ITK
accessor method is now invoked.
Added methods for converting pixel/component types

the itkBioFormatsImageIO class now has methods to convert the
Bio-Formats pixel types to ITK components, and back.
Unflipped little/big endian setting

itkBioFormatsImageIO was setting big endian when the image was little,
and little when it was big. This has been reversed.