Bump to pom-scijava 1.150

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
IJ Robot is an external plugin now

As of 1d894ba9(Mark the first commit of IJ Robot in its own repository) in
the IJ Robot source code repository at https://github.com/fiji/IJ_Robot
(which was generated from this commit's parent commit), IJ Robot is an
external core Fiji plugin.

Therefore, remove the now-obsolete source code from Fiji's source code.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Remove obsolete zs directory

Those sources have not been compiled for some time now. Apparently
they are not needed any longer.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add Vaa3d Writer as external plugin

This is the first external plugin that was developed using Maven
completely independently of Fiji. Nice.

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

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
MiniMaven is a standalone project now...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
TrackMate 2.2.0 was just released!

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.151

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
fiji-compat really depends on ij1-patcher

Let's not rely on it being a transitive dependency...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Prepare fiji-lib for a redesign of Debug#run() and Debug#runFilter()

The ij1-patcher project -- which did not exist earlier, and which
benefitted from the lessons learnt from writing fiji.Debug's run() and
runFilter() methods -- is now the vastly superior way to run
encapsulated ImageJ 1.x plugins, exploiting the runtime patching of the
ImageJ 1.x classes to allow formerly impossible ways to extend ImageJ
1.x.

So let's add the dependency and switch the way we do things in
fiji.Debug to the ij1-patcher way in the next few commits.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Do not use DefaultLegacyService for runtime patching ImageJ 1.x

It is now superseded by ij1-patcher's LegacyInjector.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Replace fiji.Debug's run method with one based on ij1-patcher

We used to do our own home-brewed thing. The experience was valuable,
though, contributing vastly to what eventually became the ij1-patcher
project. Let's now use the matured ij1-patcher to do the same thing we
did before, just better.

Incidentally, this also addresses the problem that setting plugins.dir
to the Maven output directory found 'duplicate plugins' because the
classes were found both in target/classes/ as well as in
target/<artifactId>-<version>.jar.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a unit test to verify that fiji.Debug#runFilter() works as advertised

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fiji.Debug: Handle relative image paths correctly

When a user calls Debug.runFilter() with a relative image path, obviously
that image path should be relative to the project directory, not to the
directory the latest ImageJ session loaded its latest image from.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Debug: ignore plugins in $HOME/.plugins/

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'fiji-debug'

This topic branch cleans up some loose ends after the switch to
ij1-patcher, and most notably simplifies (and partially fixes) the way
fiji.Debug works. Now, debugging your plugin from within Eclipse is as
easy as:

	public static void main(String[] args) {
		Debug.runFilter("test-image.jpg", "My Plugin", null);
	}

(assuming that you have a test-image.jpg in your project directory, and
also assuming that you added an appropriate line to plugins.config
configuring an appropriate menu item, in the example above: "My Plugin")

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Update to Sholl Analysis 3.4.1

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Support compilation with Maven on MacOSX

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.153

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Avoid accessing $HOME/.plugins in fiji-compat's integration test

Together with the upgrade to ij1-patcher 0.3.1, this fixes an
integration test reported by Jolanda Jenkins.

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