Make the Refresh File Tree command clear caches

This ensures a full refresh.

As suggested in #7929.
@dangoor Why does `ProjectManager.refreshFileTree()` need to return a Promise that waits until the refresh is done?  Is there something that needs to block on it?  Refreshing is quite asynchronous, especially if we want to include the FileSyncManager part of it too (which could wait _indefinitely_ if it needs to show a confirmation dialog).