Make the Refresh File Tree command clear caches

This ensures a full refresh.

As suggested in #7929.
Actually -- @dangoor I wonder if instead of explicitly refreshing the tree and invoking FileSyncManager, we should just have this FileSystem function close by firing a "wholesale change" event (`this._handleExternalChange(null);`).  This makes it parallel `FileSystem._unwatchAll()` even more, and we _should_ :-) already be responding to wholesale change events with a full tree refresh & file-sync anyway.