Close files earlier during full text indexing

This patch introduces a new type of message custom tailored to be caught
during each iteration of full text file indexing. This will allow us to
close these files at the close of each iteration, instead of waiting for
an entire batch of work to finish.
Move ParserSession internal to FullTextIndexer

Since there's nothing to configure for the ParserSession, we may as well
let the FullTextIndexer create a new one in its own constructor. This
*could* pose problems if more than one FullTextIndexer is running at a
time (as one ParserSession could close resources used by a different
FullTextIndexer), but currently the locking in FullTextThread precludes
this possibility.
add media type for import logs

omitting x- prefix for http://tools.ietf.org/html/bcp178
adjust how the import log is created and linked to the fileset
add upgrade script to fix old import logs

to repeat in OMERO5.0__1 for those already on OMERO5.0__0
add import log find method to the metadata service
adjust import library to use new log finding method

Conflicts:
	components/blitz/src/ome/formats/importer/ImportLibrary.java
Load log files using new method and not file annotation.
Fix copyright and space.
permit empty lists of images to be queried for import logs
add integration testing for new metadata service method
include import log in fileset graph traversal
Add Permissions to manifest (required for webstart)

Also added Codebase (currently * allows running from anaywhere) and Application-Name (displayed in the webstart dialog, instead of the user-unfriendly classname)
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]
```
Update dev_5_0 submodules

Repository: openmicroscopy/openmicroscopy
Already up-to-date.

Repository: openmicroscopy/bioformats
Updating 92e346e..1a8bced
Merged PRs (fast-forward):
  # PR 888 sbesson 'MATLAB toolbox: package and release fixes'
  # PR 882 melissalinkert 'Create bioformats_package.jar'
  # PR 856 melissalinkert 'Initial version of bfCheckJavaMemory'
  # PR 874 melissalinkert 'SDT: read each data block into a separate series (rebased onto dev_5_0)'

Repository: ome/scripts
Updating 12cb664..c0916f6
Merged PRs (fast-forward):
  # PR 64 sbesson 'Drop --use-mirrors from .travis.yml'

Repository: openmicroscopy/ome-documentation
Updating 0f8ec96..cb9e8a9
Merged PRs (fast-forward):
  # PR 647 sbesson 'Drop --use-mirrors from .travis.yml'
  # PR 642 hflynn 'Updating Demo server availability for 5.0.x'
  # PR 644 sbesson 'Add --devel option to install the OMERO 5 via Homebrew'
  # PR 638 sbesson 'Document latest changes to the Homebrew OMERO formula (rebased onto dev_5_0)'

Generated by OMERO-5.0-latest-submods#305 (http://ci.openmicroscopy.org/job/OMERO-5.0-latest-submods/305/)
Merge pull request #2058 from snoopycrimecop/merge/dev_5_0/submodules

Merging with the new Bioformats Jar (renamed in build and for MATLAB)
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