Add 'omero.import.active_close' system property

The primary blocker for this PR as a feature for 5.0.3
was that it broke compatibility with 5.0.2 servers and
earlier. Now the active closing functionality which is
needed for in-place import on Windows is *disabled* by
default, and needs to be activated via:

```
JAVA_OPTS=-Domero.import.active_close=true bin/omero...
```
Fix typo
Delegate file updating logic to updateOriginalFile

All the logic for setting the name, size, uploading bytes and performing
checksums should now be handled in updateOriginalFile. This function is called
by writeFileAnnotation as well as updateFileAnnotation.

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)
Fix call to updateService in writeFileAnnotation

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)
Merge pull request #2595 from joshmoore/12311-auto-memory

12311 auto memory
Merge pull request #2744 from mtbc/testInputs-is-flaky

mark testInputs integration test as failing
Tidy up the M files (unused variables, semicolon)

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)
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 2774 (clear sessions (rebased onto dev_5_0))