Remove legacy ome-editor and ome-notes
Simplify deprecated scripts

There is no need to document the details of their use; interested
parties can refer to the suggested alternatives for that.
Use SCIFIO_DEVEL for developer config

The bash scripts also now quote the environment variable when testing
whether it is set, which is much safer.

Lastly, the comment documenting the SCIFIO_DEVEL option has been updated
to hopefully state more clearly in exactly which circumstances you might
want to use it. (It may not be only when building from source, but any
time you want to manually set your own CLASSPATH rather than relying on
the scripts to do it for you.)
Create a common configuration script for CL tools

This provides a place to set common variables, etc., to avoid repeating
so much boilerplate between the scripts.

This change also improves the DIR computation on Windows, fixing a bug
in the backslash handling, as well as simplifying the expression.
Push Java memory configuration into common config
Move proxy server settings into common config
Skip the update check if NO_UPDATE_CHECK is set
Move SCIFIO_DEVEL notes into shared config
Use a common launch script to reduce boilerplate
Fix bug in deprecated bfview command

When the tools directory is not on the path and the CWD is not
the tools directory, the delegation to "showinf" does not work;
the fix is to use the DIR variable to specify showinf's location.
Use launch script for editor, ijview and notes

These scripts have additional JAR requirements, which we can check for
each in script, then pass them to the launcher in a new CPAUX variable.
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
Update omeul command to require ome_tools.jar

Internally, this change also accepts ome-io.jar (and implicitly its
transitive dependencies) instead of ome_tools.jar, similar to how the
launch script accepts bio-formats.jar instead of loci_tools.jar.

The script now also warns that omeul is discontinued, and comments that
the command works only with the OME Perl server.
ImageJ 1.x plugin: warn the user about Standard ImageJ being deprecated

Standard ImageJ is an obsolete format, but still there for legacy macros
and plugins. Therefore, it should not be used anymore.

To inform the user, special-case the Standard ImageJ format to output a
custom warning with a red "Warning!" label when in interactive mode.

This developer considered implementing a more general solution to
deprecate choices, but reminded himself of the YAGNI principle:
https://en.wikipedia.org/wiki/You_ain%27t_gonna_need_it
So: until the time when a more general solution is needed, the current
one should do nicely.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update version numbers to 4.5-{DEV,SNAPSHOT}
Merge pull request #156 from melissalinkert/4.5-dev-version-numbers

Update version numbers to 4.5-{DEV,SNAPSHOT}
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