Trainable Weka Segmentation: make release (2.0.0)
Fix 'mvn install -Dimagej.app.directory=...' in all Fiji projects

Ignacio Arganda-Carreras noticed that this did not work anymore after
the individual Fiji projects were split out from fiji.git.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Sort external/.gitignore

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Remove a couple of obsolete entries from external/.gitignore

A couple of those projects are no longer needed.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix external/.gitignore

We decided to skip trailing underscores from repository names,
following TrackMate's example...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump Graph_Cut to a release version

We just released a new version, and the long-term plan is to stabilize
all Fiji projects at release versions for fully-reproducible builds
anyway.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
gitignore: fix alphabetization
gitignore: add more entries

These were present after a "./Build.sh" from a clean checkout.
Use SciJava's fork of the Java Expression Parser

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Make sure that sources and javadocs are attached

Since pom-fiji serves as parent to all Fiji projects, this implies
that we now attach sources and javadocs to *all* Fiji projects from
now on. Onwards!

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Introduce 'cumulative-javadocs' profile

This is intended for the Jenkins job at:

	http://jenkins.imagej.net/job/Fiji-javadoc/

To make this work, we had to switch back from runtime-scoped
dependencies to compile-scoped ones, unfortunately.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.157

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Bump to pom-scijava 1.158

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Bump to pom-scijava 1.160

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Use the new, and improved, MiniMaven

MiniMaven moved into the SciJava realm, and it also acquired the
ability to clean out artifacts from the ImageJ.app/ directory
structure. Let's use the new version.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
wiki-monitor: handle self-signed https:// conncections

Some Wiki -- e.g. Micro-Manager's -- insist on using HTTPS albeit with
a self-signed certificate. The symptom is a long stack trace ending in

	SunCertPathBuilderException: unable to find valid certification
	path to requested target

To remedy this, download and run

	http://wiki.openkm.com/index.php/File:InstallCert.java

(e.g. java InstallCert micro-manager.org:443) and accept the appropriate
cert (typically, the first one is the correct one, so hitting the Return
key is enough).

This will generate a jssecacerts file, and thanks to the change
introduced by this commit, the wiki-monitor will pick it up.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
upload-plugin-from-maven: use the new 'install-artifact' goal

Version 0.5.0 of imagej-maven-plugin introduces the 'install-artifact'
goal which works just like 'copy-jars' except that it does not need
a pom.xml file.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Build.sh: do not consider empty files up-to-date

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Build.sh: follow redirects when downloading maven-helper.sh

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Added a conversion to 8-bit

As the original image is only white and black, an 8 bit datatype is
sufficient to store information about the picture. Changing the datatype
allows for the use of the Glasbey spectrum. When applied to a black and
white picture, the Glasbey spectrum will assign each shade of grey a
vastly different color, allowing for easy differentiation between
shades.