Descriptor based registration can run silently
Descriptor based registration returns the number of inliers when called through java
updated TrakEM2 and mpicbg submodule to their current master.  Both are
still pre-maven commits and will not build with the current builder.
However, given that they did not build before either, this commit should
not introduce a new problem.  Building it requires to apply the following
diff to the main Fakefile proposed by Johannes Schindelin

diff --git a/Fakefile b/Fakefile
index 769d8f8..ad61853 100644
--- a/Fakefile
+++ b/Fakefile
@@ -123,13 +123,13 @@ dev[./ImageJ $DEBUG_ARGS] <-

 # From submodules
 jars/ij.jar <- jars/javac.jar modules/ImageJA/
-CLASSPATH(plugins/mpicbg_.jar)=jars/ij.jar:jars/mpicbg.jar
+CLASSPATH(plugins/mpicbg_.jar)=jars/ij-1.47b.jar:jars/mpicbg.jar
 plugins/mpicbg_.jar <- modules/mpicbg/
-CLASSPATH(jars/mpicbg.jar)=jars/ij.jar:jars/Jama.jar
+CLASSPATH(jars/mpicbg.jar)=jars/ij-1.47b.jar:jars/Jama-1.0.2.jar
 jars/mpicbg.jar <- modules/mpicbg/
-CLASSPATH(jars/VectorString.jar)=jars/ij.jar:jars/Jama.jar:$JAVA3D_JARS
+CLASSPATH(jars/VectorString.jar)=jars/ij-1.47b.jar:jars/Jama-1.0.2.jar:$JAVA3D_JARS
 jars/VectorString.jar <- modules/TrakEM2/
-CLASSPATH(plugins/TrakEM2_.jar)=jars/ij.jar:jars/jai_core.jar:jars/jai_codec.jar:jars/VectorString.jar:jars/postgresql.jar:jars/jcommon.jar:jars/jfreechart.jar:jars/edu_mines_jtk.jar:jars/VIB-lib.jar:plugins/VIB_.jar:jars/mpicbg.jar:plugins/loci_tools.jar:plugins/bUnwarpJ_.jar:plugins/level_sets.jar:plugins/Fiji_Plugins.jar:jars/Jama.jar:jars/imglib.jar:jars/imglib-algorithms.jar:jars/imglib-ij.jar:plugins/Simple_Neurite_Tracer.jar:plugins/3D_Viewer.jar:plugins/Lasso_and_Blow_Tool.jar:plugins/mpicbg_.jar:$JAVA3D_JARS
+CLASSPATH(plugins/TrakEM2_.jar)=jars/ij-1.47b.jar:jars/jai_core.jar:jars/jai_codec.jar:jars/VectorString.jar:jars/postgresql-8.2-506.jdbc3.jar:jars/jcommon-1.0.17.jar:jars/jfreechart-1.0.14.jar:jars/edu_mines_jtk.jar:jars/VIB-lib-2.0.0-SNAPSHOT.jar:plugins/VIB_-2.0.0-SNAPSHOT.jar:jars/mpicbg.jar:jars/loci-common-4.4-SNAPSHOT.jar:jars/scifio-4.4-SNAPSHOT.jar:plugins/loci_plugins-4.4-SNAPSHOT.jar:plugins/bUnwarpJ_-2.6.jar:plugins/level_sets-1.0.jar:plugins/Fiji_Plugins-2.0.0-SNAPSHOT.jar:jars/Jama-1.0.2.jar:jars/imglib-2.0.0-SNAPSHOT.jar:jars/imglib-algorithms-2.0.0-SNAPSHOT.jar:jars/imglib-ij-2.0.0-SNAPSHOT.jar:plugins/Simple_Neurite_Tracer-2.0.0.jar:plugins/3D_Viewer-2.0.0-SNAPSHOT.jar:plugins/Lasso_and_Blow_Tool-2.0.0-SNAPSHOT.jar:plugins/mpicbg_.jar:$JAVA3D_JARS
 plugins/TrakEM2_.jar <- modules/TrakEM2/
 plugins/ij-ImageIO_.jar <- modules/ij-plugins/

Then, call ./Build.sh; ./Build.sh jars/mpicbg.jar;
./Build.sh plugins/mpicbg_.jar; ./Build.sh plugins/TrakEM2_.jar

and delete the corresponding mpicbg and TrakEM2 SNAPSHOTS in plugins
Merge branch 'master' of https://github.com/fiji/fiji
descriptor based registration can be called from other plugins easier
Merge branch 'master' of ssh://fiji.sc/srv/git/fiji
using modified outofbounds
Merge branch 'master' of ssh://fiji.sc/srv/git/fiji
Bug Submitter: the URL changed to http://fiji.sc/bugzilla/

This is simpler, and it was also easier to set up when upgrading Bugzilla
to version 4.2.3.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bug Submitter: include newlines in the .html output

... which is only shown in case of error, of course.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bug Submitter: also include the edit token

... as required by Bugzilla (at least version 4.2.3); for good measure,
include two more form entries.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fiji Updater: be a little bit more verbose

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fiji Build: recognize mpicbg-20111129.jar as a versioned file

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
3D Viewer: Make orthoslices opaque via the transfer function.
Merge branch 'master' of git://fiji.sc/fiji
3D Viewer: Update build script for the IJ1 version of the plugin.
Adjust analyze-dependencies.bsh to the ImageJ updater

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Adding old files
Mask respects the fit curve option
Foreground (target) color is now always non-zero
Fixed DoSpikeSupretion
 - targetpoints were never compared in stair checks
 - DoSpikeSupressio is no longer an option, as it is relatively fast
Code cleaning