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.
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}
Add missing set commands to commented-out code
Do not gratuitously set Windows environment vars
Add new files to bftools.files list

This ensures they are included in the bftools.zip distribution.
Use fork=true to fix Windows build
Use SCIFIO_MAX_MEM variable for max heap size

This avoids overwriting an existing JFLAGS variable, but rather appends
it with "-Xmx$SCIFIO_MAX_MEM", and using a default of 512m if not set.

Now the config script does not overwrite *any* environment variables by
default; the user needs to edit it for it to actually do anything.
Isolate environment variables using SCIFIO_ prefix

Variables have been renamed as follows:
  * CPAUX -> SCIFIO_CP
  * DIR -> SCIFIO_DIR
  * JFLAGS -> SCIFIO_FLAGS
  * PROG -> SCIFIO_PROG

This makes name clashes much less likely. All of these variables are
completely overwritten by the scripts, so setting them a priori will
have no effect (except in the case of "SCIFIO_PROG=xyz launch.sh").