Add JvmSettingsCheck on startup of Java components

Max. memory, OS memory, and the number of processors are
now printed on startup. This should help to debug cases
where the Xmx settings for the processes have not been
reset in production.

See:
https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=6471
Fix indent
Do not always expand the tag nodes.
Fix RTypesI.{cpp,h} whitespace
Fix whitespace in PermissionsI.cpp
Fix default permissions from string

PermissionsI.perm1 wasn't being properly initialized
leading to invalid trues from the getter methods.
Use explicit "omero.group" rather than -1

In gh-984, @rleigh-dundee saw testAdjustPermissions fail
periodically, likely caused by the default group of the root
user.
Include JvmSettingsCheck in startup
Add java.version and os.* to INFO
Do not automatically the user.
Do not modify the default group when logging out.
Save after clicking on the save button.
Remove whitespace
add fail's and adjust whitespace
Add support for more repo in menu.
Don't use omero.group=-1 when not required (Fixes #11427)
merge dev_4_4 -D org -I include -E exclude: PR 1126 (Fix long-missing DELETE EventLogs)
merge dev_4_4 -D org -I include -E exclude: PR 1430 (fix #10564: include wells in plate run processing)
merge dev_4_4 -D org -I include -E exclude: PR 1450 (Update log jars)
merge dev_4_4 -D org -I include -E exclude: PR 1459 (Scripts menu 11434)