FS-lite file security

This branch provides intermediate fixes for the the FS-lite based import in 4.5 before a major refactoring.  Most (though still not all) of the methods in `PublicRepositoryI` now take the database into account rather than relying on the actual OS filesystem. Directories are now created for all intermediate paths and are secured via the repository implementation.

I've tested regular import and the script service. A screen import still needs to be done. You can check that the directory names created will have odd increments like "``-2``" under ``/OMERO/ManagedRepository``.

Otherwise, nothing should have changed for the clients though one can expect more exceptions in certain situations (directory already exists, etc.)

/cc @chris-allan, @knabar, @will-moore, @jburel, @ximenesuk , @bpindelski, @mtbc