renaming-merge: allow merging from a local branch

Very useful, e.g. when importing .zip files and merging them into
a subdirectory...

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

After installing VirtualBox (https://www.virtualbox.org/) and Vagrant
(https://www.vagrantup.com/), developers can use

	vagrant up

to obtain an Ubuntu development environment that can build Fiji --
regardless of the current host operating system.

This development environment is a dedicated, headless VirtualBox
instance into which -- once started up via 'vagrant up' -- the developer
can log in vi 'vagrant ssh'.

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

This makes it easy to obtain an Ubuntu Linux virtual machine by running
'vagrant up' followed by 'vagrant ssh'. It only requires VirtualBox and
Vagrant to be installed.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a script to keep the 'TrackMate-dev' update site up-to-date

This script is intended to be run by this Jenkins job:

	http://jenkins.imagej.net/view/Fiji/job/TrackMate-dev-update-site

A couple of things are left to do for the future:

- reconcile with upload-update-site.sh

- avoid the "dummy" hack by teaching MiniMaven to install artifacts from
  remote repositories (without having to make them dependencies first)

- fix the bug in MiniMaven that makes it remove miglayout-swing.jar

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
upload-update-site: restructure update-site information handling

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.118

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Fiji_Uploader: update IJ2 package

Updated the SampleImageUploader package from imagej.core.commands to
imagej.plugins.commands.
Allow calling fiji.Debug.run() from test classes

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
fiji.Debug#run(): make sure that ij-legacy had a chance to patch ImageJ 1.x

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Migrated SPIM Registration to its own repository at:
    https://github.com/fiji/spimreconstruction
Add forgotten property

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
added the current version of SPIM_Registation to the main pom.xml
Merge branch 'master' of github.com:fiji/fiji
updated required version of SPIM_Registration for the Descriptor_based_registration
Ignore if spimreconstruction is cloned into externals/

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

We use Unix sorting in the properties, i.e. upper-case letters are
sorted before lower-case (so that Z still goes before a).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
jep moved to its own repository

It lives in https://github.com/fiji/jep now, the current commit is
b76f4a1d(Update SCM location).

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