Move to JGraphx version 2.3.0.5

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Move to JGrapht version 0.9.0

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'master' of git://github.com/fiji/fiji
Revert "Move to JGrapht version 0.9.0"

This reverts commit e5d54c619b3f90142a744fb9cf2d203d46776826.
Revert "Move to JGraphx version 2.3.0.5"

This reverts commit 6fc6e0e5f8af7ca7ffe6e2453969f7be617c22eb.
Consolidate Bio-Formats update site script

It now handles Bio-Formats 5 updates from the dev_5_0 branch.
Build.sh: Temporarily bump MiniMaven version to -SNAPSHOT version

The long-term plan for MiniMaven is to live in its own repository, being
versioned independently of ImageJ. Once that is the case, we can easily
bump MiniMaven to a new version and use it in Build.sh when critical bugs
were fixed, such as the one Jazz Jenkins identified today. For the moment,
though, let's just go for a snapshot version and fix accordingly once
MiniMaven lives in its own repository.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of git://github.com/fiji/fiji
Bump to pom-scijava 1.142

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Build.sh: use the shiny new MiniMaven

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.147

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Bump to pom-scijava 1.148

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Use new ij1-patcher version

This will be needed for the upcoming fix to bin/write-headless.jar.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Adapt bin/write-headless-jar.bsh to new ij1-patcher

Things are now a bit different. Easier, too.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Teach write-headless-jar a full and/or non-headless mode

It is really handy to have an ij1-patched drop-in replacement for ij.jar
in case you cannot modify the startup procedure as the ImageJ launcher
does. This change allows you to write that with

	write-headless.jar --no-headless --full-jar patched.jar

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix FijiTools.isDeveloper()

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Let FijiTools#getFileExtension hand off to scijava-common

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Avoid overriding the legacy initializer

A much better way is to let LegacyInitializer do its job and declare
a service (that we might want to use for more Fiji-specific stuff
later) that the SciJava Context will discover and initialize.

That way, Fiji gets handled properly even when started from a patched
ij.jar written out by "write-headless-jar --no-headless --full-jar"
(because we no longer have to override things before starting the
LegacyEnvironment, or for that matter, patched ij.ImageJ).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'write-headless-jar'

This topic branch fixes ./Build.sh misc/headless.jar and makes the startup
of Fiji more robust by avoiding a Fiji-specific override of the default
startup procedure of ij1-patcher & ij-legacy.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
ImageJ.sh: support the --debugger option of ij-launcher, too

The --debugger option comes in real handy when debugging in Eclipse.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>