I sort many of my messages into folders and subfolders by using rules. While I do use a Search Folder to keep track of all the new messages, the new messages still expand the folder list which is fairly large.
The result is that the Navigation Pane looks quite cluttered and it pushes my other mailboxes down and out of view and I need to scroll down to see them.
Is there a way from preventing these subfolders from being opened or to quickly collapse them all at once?
Preventing subfolders from being opened, when a new message arrives, is only possible if you have marked them as a Favorite folder. As you are talking about many subfolders here, this is probably not really a solution in this case.
A quick method to collapse all opened subfolders at once is to collapse the root of your mailbox and then expand it again.
To do this, simply click on the arrow or the – (minus) icon in front of the top level folder of your mailbox. To expand it, click the arrow or + (plus) icon again. This will now only show the folders which are directly under the mailbox and subfolders will remain collapsed.
No matter how deep your folder level structure has been opened, collapsing and then expanding the mailbox root will collapse any opened subfolder.