Test directory delete

In order to move the top level directory, first
it was necessary to check that the empty directory
would be removed from disk.
Move dir deletion into prep_directory
NB: improve callback/handle closing in submit

There are a number of error conditions where
neither the handle nor the callback object
from client.submit() will be returned to the
user. Since the exceptions do not include the
objects and it was not a part of the "API" to
require a `close()` we will make a best effort
at cleaning up resources when an exception
occurs.
Update dev_5_0 submodules

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

Repository: openmicroscopy/bioformats
Updating e598e14..0cb78d9
Merged PRs (fast-forward):
  # PR 1201 melissalinkert 'Leica LIF: do not set Channel.Color for RGB images (rebased onto dev_5_0)'
  # PR 1198 melissalinkert 'ScanR: fix exposure time units (rebased onto dev_5_0)'
  # PR 1197 melissalinkert 'Add modulo support for LI-FLIM data (rebased onto dev_5_0)'
  # PR 1202 melissalinkert 'DICOM: fix units for physical sizes (rebased onto dev_5_0)'
  # PR 1196 joshmoore 'Close IFormatReader copy if not to be used'
  # PR 1188 mtbc 'AFI: populate magnification and physical pixel size metadata (rebased from develop)'

Repository: ome/scripts
Already up-to-date.

Repository: openmicroscopy/ome-documentation
Updating db2db83..8004c06
Merged PRs (fast-forward):
  # PR 852 hflynn 'Tidy Upgrade page incl. Paris requests for 5.0.3'
  # PR 819 joshmoore '12311 auto memory docs'
  # PR 853 sbesson 'Document orphaned datasets/plates retrieval via getProjects/getScreens'
  # PR 855 aleksandra-tarkowska 'Session engine (rebased onto dev_5_0)'
  # PR 836 mtbc 'Managed repository template path expansions'
  # PR 848 aleksandra-tarkowska 'Nginx doc (rebased onto dev_5_0)'
  # PR 851 aleksandra-tarkowska 'adding HTTP response header (rebased onto dev_5_0)'
  # PR 844 hflynn 'Re-working OMERO sysadmin index page'
  # PR 847 hflynn 'Reformatting VA docs to make them less scary '
  # PR 842 sbesson 'Insert OMERO sidebar template after page TOC sidebar'

Generated by OMERO-5.0-latest-submods#442 (http://ci.openmicroscopy.org/job/OMERO-5.0-latest-submods/442/)
Include only dir and log in tomove
Fix test_fs after changes to get_fileset
Fix flake8 err
merge dev_5_0 -D org: PR 2242 (Use mklink under Windows)
merge dev_5_0 -D org: PR 2596 (Groups users menu 12082)
merge dev_5_0 -D org: PR 2615 (Sphinx api improvements)
merge dev_5_0 -D org: PR 2667 (Add a quiet option to CLI commands)
merge dev_5_0 -D org: PR 2676 (Overhaul of Insight's Search, Part 2)
merge dev_5_0 -D org: PR 2678 (Matlab CZI job)
merge dev_5_0 -D org: PR 2681 (12252 script limit)
merge dev_5_0 -D org: PR 2693 (Mousewheel zoom centres on mouse location)
merge dev_5_0 -D org: PR 2726 (Preview fix)
merge dev_5_0 -D org: PR 2741 (add trivial checksum algorithm that reflects file size only)
merge dev_5_0 -D org: PR 2743 (`fs rename` command for modifying template values)
merge dev_5_0 -D org: PR 2759 (Update dev_5_0 submodules)
merge dev_5_0 -D org: PR 2769 (Auto close)