Refuse to alter read-only elements at runtime

In the Element.set() method, check whether the element being altered
is from a read-only file. That should only ever happen when
(re)loading of files is underway, either at start time or because
the reload command/SIGHUP has been issued. If an attempt is made to
change a read-only element at any other time, raise a
PermissionError exception instead of setting the new value in memory
(altered values were never written to the backing file, but prior to
this it was possible to modify the in-memory copies).