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config: fix wrong status after setting permissions

Before this patch, it was possible that the config status could change
to 'ready' even if there were pending alerts. This could happen if there
were 'missed_privilege' warnings. Before this patch, warnings were
cleared and then refilled if necessary. However, after clearing all
these warnings, if there were no other warnings, the status was set to
'ready'. And if new warnings were added during the 'refilling' stage,
the status did not change from 'ready' to 'check_warnings' or
'check_errors'.

Part of #9689

NO_DOC=bugfix
NO_CHANGELOG=unreleased bug

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