opem

Having the same issue. After updating, both Alfred and Spotlight was missing a whole bunch of apps (such as Photoshop and Activity Monitor). I've cleared cache, rebuilt metadata, relaunched the software, double-checked Spotlight settings, and made sure the scope is correct--which it obviously is, since several applications in the same folder(s) pop up. I'm still missing the above-mentioned apps. (OS X 10.8.5)