Consider following situation:

I'm setting preferencesId as my package identificator: foo.bar, and I expect it to work as usual preferences API, so the every package level should have separate directory, but it's not:

$ ls ~/.java/.userPrefs/
... foo.bar ...

while expected is

$ ls ~/.java/.userPrefs/
... foo ...
$ find ~/.java/.userPrefs
.../.java/.userPrefs/foo
.../.java/.userPrefs/foo/bar
.../.java/.userPrefs/foo/bar/JVMUserOptions
.../.java/.userPrefs/foo/bar/JVMUserOptions/prefs.xml

As I have the workaround (use "foo/bar") priority may be low.