upload-update-site.sh: detect executable to use

The Bio-Formats update site Jenkins jobs failed today because
ImageJ-linux64 was missing, even though fiji-linux64 was still present.
Probably there was a change in the Fiji update site configuration. But
regardless, let's be more thorough about detecting which executable to
use for uploading the update site, rather than hardcoding 64-bit Linux.
upload-update-site.sh: add check for launcher

If the launcher is not present, fail fast.
upload-update-site.sh: remove bashism

It seems that double equals is bash-specific, whereas single equals is
OK. I probably knew this once or twice, but forgot... again.
upload-update-site.sh: do not use "fiji" launchers

The reason is that the fiji launchers just hand off to the ImageJ
launcher anyway. So if the ImageJ launcher is not present, they will
fail regardless.
upload-update-site.sh: download Fiji earlier

If Fiji has not been downloaded yet, we should download it, *then* check
for the ImageJ launcher. Otherwise it will always be missing, of course.
upload-update-site.sh: fix test for Fiji dir

The test was inverted.
IO: add the SCIFIO importer plugin

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
gitignore: use wildcard for mapdb version
Bump to pom-scijava 1.114

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Remove all .factorypath files

Now that we no longer use SezPoz but SciJava-common's own annotation
processor, let's not force a specific (forked) SezPoz version into
Eclipse's factory path.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Adjust SCIFIO reader to new SCIFIO version

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Remove Eclipse-specific annotation processor settings

These were needed as long as we had SezPoz...

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
SCIFIO_Reader: add null img check

Although the IO class no longer throws exceptions, its returned ImgPlus
can be null.

Added a check for null.
SCIFIO_Reader: check for null arg

arg is tested for being an empty string, and if so the show() command is
invoked. However, arg can be null at the point of this test. So, if it's
null or empty, we invoke show. Otherwise assume it's being run headless
as a file was passed.
Bump to pom-scijava 1.115

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Bump to pom-scijava 1.116

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Batch Weka Segmentation: Re-run an interrupted job without redoing unnecessary work
Archipelago: Bugfixes and workarounds

SIFT Point match parameters are bottled directly to work around problems with inpersistence in Serialization.
Cluster Processes are now ack'd, to prevent miscommunication from hanging a cluster run.
Fixed a concurrency bug in ArchipelagoFuture that was causing cluster runs to hang.
Made point-id mapping more reliable in clusterized instances of elastic alignment.
Fiji Archipelago: Uniquely-named client node logs, as per David Hildebrand
Trainable Weka Segmentation: added variation of information metric.

For now, it has methods to calculate the variation of information between 2D segmentations (images or stacks). This implementations uses the N^2 normalization and the foreground restriction. For 2D stacks, the metric value is the average of the variation of information through the slices.