Comparing strings and integers with `is` is a bug: comparisons should be
done with `==`. It might not have caused observable problems in the past
because small integers and strings can be interned.
Previously, clean read the defaults once, and then it updated the
setting for each entry it read. This resulted in the defaults being
clobbered and then not being respected for subsequent entries. This
patch fixes the issue by re-reading the defaults before processing each
item.
The other plugins (link, shell) do not have this problem.
