Bump to pom-scijava 1.88

This updates the SCIFIO dependency to 0.7.1, which fixes an
inconsistency between ImgLib2 dependency versions (SCIFIO 0.7.0
depended on ImgLib2 2.0.0-beta-19, but ImageJ2 depended on
2.0.0-beta-20, which was not backwards compatible due to the
removal of the old calibration API).
AbstractIOPlugin: add missing final keyword
Bump to pom-scijava 1.89

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
minimaven: support "bundle" packaging

A "bundle" is just an OSGi-ified JAR file, so we should treat
them the same as regular "jar" bundling for our purposes.
Merge branch 'bundle-packaging'

This lets MiniMaven handle JARs which are OSGi bundles.

Specifically, it avoids an issue with log4j dependencies being ignored
(and hence not added to downstream JARs' MANIFEST.MF classpaths) due to
the packaging being "bundle" rather than "jar" as usual.
Bump to pom-scijava 1.90

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Revamp the ConsoleService

As per ticket #1212, the ConsoleService has moved from ij-app to
ij-core. The two currently supported arguments "--open" and "--run" have
been split into their own ConsoleArgument plugins, with additional
plugins being possible in other components and extensions of ImageJ.

This change also has the added benefit of removing concrete plugin
implementations from the ij-app component. For technical reasons it is
difficult to generate the imagej uber-JAR properly when the ij-app
aggregator component itself contains concrete plugin implementations.
So with this change, the uber-JAR is functional again.
Merge branch 'console-args'

This branch revamps the ConsoleService to be modular in nature,
adding a new ConsoleArgument plugin type that extends the
capabilities of ImageJ's command line options.
Bump to pom-scijava 1.91

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
QuitProgram: avoid service calls after dispose

Technically there was no explicit bug here, but calling any method of a
service after the context has been disposed seems best to be avoided. So
this change reorders the execution flow so that the dispose() call is
the last thing to happen (except for maybe a System.exit(0) afterward).
Updater (cmd-line): use the LogService consistently

Only for interactive input, we still use System.err. Otherwise we
log messages, properly prefixed, via the LogService from now on.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Updater (cmd-line): support simulating uploads

This adds the --simulate option to the 'upload' command.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Updater (cmd-line): optionally forget missing dependencies upon upload

This adds support for the --forget-missing-dependencies option when
uploading: It will force the updater to break the dependency whenever a
dependency goes missing.

This option is intended primarily for automated uploads, e.g. the
Bio-Formats daily site.

The reason for this change was that the Bio-Formats daily site could no
longer be updated properly when the netcdf dependency was renamed into
netcdf-java: the updater believed that bio-formats needed both and
complained that netcdf-java was no longer there.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Updater: clean up code

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

This topic branch was triggered by the failure of the Jenkins job
updating the Bio-Formats daily update site due to a renamed dependency.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Bump to pom-scijava 1.92

Signed-off-by: Jenkins <jenkins@dev.loci.wisc.edu>
Merge branch 'master' of https://github.com/imagej/imagej