Use mklink under Windows

In order to support in-place importing on Windows, mklink
rather than ln must be used. Rather than create new commands
like `--transfer=mklink`, the same flags (`ln` and `ln_s`)
are being used.
Fixes from jh713@cam.ac.uk

 * cmd /c is needed to call mklink from Java
 * Arguments need reversing.
Close file handle before attempting delete

@bpindelski showed that on Windows the UUID-containing
file created by checkLocation was not being properly
deleted during import. This change closes the RawFileStore
and then re-opens in order to allow in-place import under
Windows.
Print command and stdout/err on error

The stdout and stderr (which are merged) are now read
from the created Process instance if the return code
is not 0.
Silently ignore ObjectNotExistException

If `checkLocation` throws an exception, then
`cleanupUpload` will definitely throw an ONEE
since the proxy no longer exists. Cleaner would
be to null some instance variable, but due to
the possibly multi-threaded nature of the Transfer
object, we're doing something simpler here.
Remove ManagedRawFileStoreI in favor of callbacks

ManagedRawFileStoreI was not being used which meant that
closeCalled was never invoked and therefore the proxies
in `ManagedImportProcessI.uploaders` were never cleaned.
This led to `ObjectNotExistException` being thrown on a
second loading of `proc.getUploader(i)`. Rather than add
logic to create the correct subclass of RepoRawFileStoreI,
a callback interface has been added which can be used for
any implementation.
Merge 'origin/dev_5_0' into windows-in-place

Conflicts:
	components/blitz/src/ome/services/blitz/repo/RepoRawFileStoreI.java
refactor path terms that make new directories, make %time% one
start next-directory index search from 0 to match docs
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
Clarify checkLocations's error conditions

In order to prevent confusing messages after a
`FileUtils.deleteQuietly()`, we actively throw
an exception for all the in-place import types.
make changes compatible with Ice 3.3
move path-directory-making to path package
Fix stupid typo in search.include_types
Improve messages on in-place failure conditions
Merge pull request #2790 from joshmoore/event-log-fix

Fix stupid typo in search.include_types
Merge pull request #2773 from mtbc/trac-11096-import-dir-uniqueness

fix #11096: ensure that new %time% directory is unique
Merge pull request #2242 from joshmoore/windows-in-place

Use mklink under Windows
Update dev_5_0 submodules

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

Repository: openmicroscopy/bioformats
Updating e598e14..06f23c9
Merged PRs (fast-forward):
  # PR 1207 rleigh-dundee 'docs: Merge xsd-fu prerequisites into build instructions'
  # 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..53a820a
Merged PRs (fast-forward):
  # PR 860 mtbc 'move %time% template expansion term to only user-owned'
  # 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'

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