Switch reindexer to use slf4j.
Exit quickly if files are inappropriately added

When using `--wait_completed` and `--close_completed`,
no files are accepted on the command-line. Rather than
silently ignore them, this commit now exits with an ERROR.

```
($ bin/omero import -- --close_completed foo bar
 INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-rc1-DEV-ice35
 INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-rc1-DEV-ice35 revision: 92e346e date: 6 February 2014
 INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
 ERROR  formats.importer.cli.CommandLineImporter - Files found with completed option: [foo, bar]
```
Fix imaje2 typo
Fix NPE using `apt-get install imagej`

The `/usr/bin/imagej` launcher under Ubuntu starts
ImageJ and points it at the directory `~/.imagej`
to look for plugins. The location `./plugins` doesn't
exist, and so the insight code receives a null array
of locations. This is just a workaround; perhaps later
versions can look for the `~/.imagej/plugin` directory
itself. (There may be a System property that points to
the location set via -ij_user_path)
Merge pull request #2058 from snoopycrimecop/merge/dev_5_0/submodules

Merging with the new Bioformats Jar (renamed in build and for MATLAB)
Allow loci_tools or bioformats_package as dependencies.
Fix dual dirs in the mac zip for insight

gh-1994 re-introduced importer-cli but at the same
time used `${main-dist-prefix}` rather than
`${dist.zip.prefix.osx}` leading to split directories.
Change signjar task to apply/exec jarsigner with custom args

The ant signjar task doesn't support -storepass:file.
Note this no longer preserves the original file modification time.
Replace jarsign.storepass property with jarsign.storepassfile

Added default password file lib/keystore.passwd
Merge pull request #2070 from ximenesuk/reindex-logging

Switch reindexer to use slf4j.
Replace genkey task with exec keytool -genkey

Need to use -storepass:file
Add jarsigner timestamping
Set default timestamping authority to http://time.certum.pl
Exclude B-F and logback jars.
Separate PluginLoggerImpl from LoggerImpl

Since all methods in LoggerImpl were checking
`if (runAsPlugin < 0) {...}` separating out the logic
into a separate class is straight-forward. The reason
for doing this, however, is that in the case that the
IJ plugin is used with the `loci_tools.jar` jar, which
contains log4j, then the client hangs at

    "Loading Logger Service"
Merge pull request #2059 from jballanc/close-parsed-files

Close parsed files after each indexing iteration  (fixes #11949)
merge dev_5_0 -D org -I include -E exclude: PR 2055 (fix #11877: move import logs to upload jobs instead of annotations)
merge dev_5_0 -D org -I include -E exclude: PR 2069 (Insight manifest changes for webstart #11772)
merge dev_5_0 -D org -I include -E exclude: PR 2071 (Final in-place fixes)
merge dev_5_0 -D org -I include -E exclude: PR 2073 (Fix dual dirs in the mac zip for insight)