Make the Refresh File Tree command clear caches

This ensures a full refresh.

As suggested in #7929.
I just reduced the implementation based on your suggestion and then realized that this solution doesn't fix the case where a FileSystem change event handler is broken and throwing exceptions (which is the case I was testing with via a purposefully bad extension). If the event doesn't make it through, the tree never refreshes.

That said, I like this implementation better and think that what we want is this implementation plus more robust event handling.