Have raw file bean flush file metadata.

This commit is rebased back from develop.
Trivial formatting rebased from #995
Merge pull request #1021 from mtbc/trac-10602

Have raw file bean flush file metadata.
Merge pull request #1023 from mtbc/trac-10338-trivia

Trivial formatting rebased from #995
Fix Homebrew uninstallation and move virtualenv/ to support folder

The last OMERO-homebrew-{stable,develop} jobs have been fail when calling
`bin/brew doctor` with a "Warning: You have uncommitted modifications to
Homebrew". This PR applies the uninstallation mechanism suggested in the
Homebrew installation script.
Additionally, a VENV_DIR variable is defined to extract virtualenv into a
proper support.
Merge pull request #1028 from sbesson/homebrew_uninstall_hudson

Fix Homebrew uninstallation
Add functions to read plate annotations
Add functions to read screen annotations
Add functions to read dataset annotations
Add functions to read project annotations
Merge pull request #1035 from sbesson/10687_plate_annotations

Add functions to read annotations (see #10687)
Merge pull request #1024 from jburel/xml-annotation

Xml annotation
Fix download text.
Add name option to download.
Review download of image sequence to allow to set the name.
Check file with same name already exists.
Review file loading sequence.
Clean code.
Make sure the loader is created only once.
Remove print out.