CLI bug fixes (rebased onto develop)



This is the same as gh-2184 but rebased onto develop.

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Various dangling CLI tickets from 5.0:

### 12024 ###
http://trac.openmicroscopy.org.uk/ome/ticket/12024 to filter inactive users:

```
$ bin/omero user add -e "test@example.com" emailtest Email Tester sudotest
Please enter password for your new user (emailtest): 
Please re-enter password for your new user (emailtest): 
Added user emailtest (id=802) with password
$ bin/omero user email -i
test@example.com, ...other addresses...
$ bin/omero user email -i --all
test@example.com, ...other addresses...
$ bin/omero group removeuser --name user emailtest
Removed 802 from group 1
$ bin/omero user email -i
...other addresses...
$ bin/omero user email -i --all
test@example.com, ...other addresses...
```

### 12002 ###
http://trac.openmicroscopy.org.uk/ome/ticket/12002#comment:5
```bin/omero config``` operations should now only save once and that they do via write-and-rename.