Pictures folder appears as a bundle?
I'm still not sure how the Pictures folder came to believe it was an iPhoto bundle. Most of the cleanup was just restoring an older version of the Pictures folder from Time Machine.

To turn the Pictures bundle back into a folder, I took the SetFile executable from my Mac (ships with the developer tools) and executed SetFile -a b Pictures.

This is important, because Mac OS will prohibit most actions done against basic folders in the user directory structure. You cannot move or delete the Pictures folder (and if you sudo your way through it, you will be missing some extended attributes on your new folder), so turning it back to normal was an essential step.