I have considered using a side by side panel design. A list of rules on the left, and a tree navigation on the right - however the tree structure could get very nested. I am concerned how a user would select multiple folders in the tree and then be able to apply the rule to all of those items / folders. Traditionally, in a tree you would click to select, but when you can pick and choose do you add a check box next to each item / folder? This feels like to could get pretty messy.
Any thoughts or suggestions on this one?