Love it! Any chance the tree view in the bundle editor could similarly show shortcuts and tab triggers?
And for that matter reuse the new dir/sub-dir format. Some of the bundles (Rails/Ruby/etc) are getting mighty hard to navigate in there.
Couple notes also:
When a bundle is selected above the tables you see "No Item Selected", "Edit Menu Structure: Ruby on Rails" might be better.
Your allowed to edit the names of items in the menu structure editor, but not of the excluded items, annoying.