CLM: AreaList Crop plugin support for multiple arealists, setting background value
CLM: Check ImageProcessor bounds before copying pixels
Archipelago: Change cluster file extension from cluster to arc
Archipelago: Added utility methods, moved some to a new Utils class
TrakEM2 Archipelago: Support new Fiji Archipelago and TrakEM2
Fiji Archipelago: Allow objects, esp nonserializables, to be translated transparently to client nodes and back.
Merge pull request #49 from larrylindsey/fiji-archipelago-summary

Fiji Archipelago Updates
Upgrade to commons-math 3.2

This version is available from Maven Central as commons-math3 with a
different package prefix: org.apache.commons.math3. This has the
advantage of avoiding conflict with Apache Commons Math 2.x, which is
also available as artifact commons-math with package prefix
org.apache.commons.math.

The three plugins that depend on commons-math (Script Editor, Simple
Neurite Tracer and Trainable Segmentation) were updated to use the new
package prefix and API where applicable.

Right now, there is nothing in Fiji core that uses commons-math 2.x,
but thanks to the package shading, it is now possible for third party
plugins to depend on 2.x without interfering with the ones using 3.x.
gitignore: rename commons-math to commons-math3

This goes along with a1b4545d8f8f705943b531b1b6566fd8b5763b14.
Save and load Script Editor preferences

This saves and loads Script Editor preferences in ij.Prefs for
tab size, font size, line wrap, emulated tabs, and window size.
TextEditor: restore Python-specific behavior

The previous commit eliminated the Python-specific tab size reset logic.
It used to be that every time Python was selected as a language, or a
Python script was opened, tab size would be reset to 4; and for other
languages, it would be reset to 8.

This change restores the Python reset to tab width 4, but changes all
other languages to restore to the saved tab size preference instead.

Hopefully this is an acceptable short term compromise for the "Python
should be width 4" convention, while still enabling tab size to be
persisted as a preference in general.
upload-bf5.sh: add version suffix to JWlz

Previously it had no version suffix, but the latest
develop branch now has that JAR with version suffix.
Merge pull request #50 from fiji/script-editor-prefs

Save Script Editor preferences
Add 3 new local threshold methods: Constrast, Otsu and Phansalkar

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'auto-local-threshold'

Thanks Gabriel!

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.106

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
loadPreferences() now uses default window width and heights if getSize() returns 0 for either dimension. Fixes bug in Ubuntu 12.04 where Script Editor is initialized with 0 pixel window.
Merge pull request #53 from sinverso/ScripEditorDefaultWindowSize

Script Editor Default Window Size
Bump to pom-scijava 1.111

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Remove obsolete Imglib Algorithm Launcher

It was based on ImgLib1, and did not use a proper plugin discovery
mechanism. We now have SciJava Common and use it with ImgLib2, which
will make discovery of ImgLib2 algorithms *truly* extensible.