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.
Switch reindexer to use slf4j.
Merge pull request #2058 from snoopycrimecop/merge/dev_5_0/submodules

Merging with the new Bioformats Jar (renamed in build and for MATLAB)
Merge pull request #2070 from ximenesuk/reindex-logging

Switch reindexer to use slf4j.
Merge pull request #2059 from jballanc/close-parsed-files

Close parsed files after each indexing iteration  (fixes #11949)
Update dev_5_0 submodules

Repository: openmicroscopy/openmicroscopy
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Repository: openmicroscopy/bioformats
Updating 1a8bced..c288aa8
Merged PRs (fast-forward):
  # PR 887 imunro 'Implement pre-loading for .sdt files in the interest of performance.'

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