Hey JD,
Was there ever a resolution to this? I used Quicksilver as my app launcher that allowed me to index special folders (like Yummy FTP bookmarks) regardless of location but have switched to Alfred due to a lack of development on Quicksilver - Alfred uses Spotlight's index for finding files and cannot launch Yummy bookmarks.
As context to previous comments, I have over 130 bookmarks so trying to find the one I want from either a dock folder or from the Yummy program is tasking, especially if Yummy is not focused, I then need to focus yummy, click Bookmarks, Choose the bookmarks folder, scroll to find the one I want and select it. It adds ~10sec a few dozen times a day. I'm going to switch back to Quicksilver until I can figure out how to get Spotlight / Alfred to index these but it's not ideal.
- Jace

(repost - previous post was to the wrong thread)