OK.. good news and bad news.... Good news is that you didn't blow away anything in /system. Had you torpedoed something in the /system partition, it would have required you to reload the factory image using a tool like Odin, etc.
Bad news is that your user data partition is now corrupted. By removing the app directory, you cut off a lot of your user data at the knees. If I was a betting man, I would say that a factory data reset will 'fix' the problem as it will format the userdata partition (which /data is part of) and recreate it. If you can, I would save off anything you want to keep and hasn't been backed up to a computer, because that all goes bye-bye when you reset.