I find the icons too big and am constantly scrolling to get to things....especially when trying to drag and drop.
There are lots of folders and files beginning with a 'dot' ( . ) Do these need to be visible from the off? can they be hidden with a tick box to allow viewing?
I also actually think that it may be better to start the tree with the 'domains folder' but at the top of the page maybe have a window where you can see the tree if you need the root folder.... It may just be me, but I am not sure many would need the root folder for everyday usage?
Most people it would be the Domains\domain.com