Fix refresh action to not reset modified flags (closes bgo#670133)
Our existing "Refresh" action piggy-backed on the reload code, using a semantically-dubious empty list to indicate a lack of changes. One upshot of this was that undo-related functionality like modified flags were unintentionally cleared on refresh. This patch breaks out minimal required refresh functionality into a new method, and replaces the old set-empty-files idiom with a call to this method.
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