Can't launch any app in Mavericks

I ran a Mac Update and a system clean-up tool yesterday and it seems to have deleted some files on my system that I am not aware of. The weird result is that now I am unable to run a few apps from anywhere on my system. However, this behavior seems to be limited to only App Store and apps that I have installed from app store (I guess) and unfortunately even the terminal app. I can still run all my web browsers like Firefox (and even Safari). I can also clear the Trash and watch movies/listen to music on VLC. System Preferences are also available.
I used to have Little Snitch before I installed Mavericks and somehow the LS settings were still active before. But I have a feeling that when I did the system clean-up, it must have deleted part of the Little Snitch files but not all the files.
Does anyone know of any way in which I could clear the entire Little Snitch settings and return my firewall and application control settings to the default?
Any help is highly appreciated! (Else my only other option is a system restore )

Yep, working on the re-install and backup ... just downloaded the Recovery Disk Assistant to keep a recovery USB drive ready as a fail-safe.
Now I upgraded from Snow Leopard to Lion to Mountain Lion and then Mavericks ... I hope a simple backup of my iLife 09 and iWork 09 apps should get it working again once I re-install Mavericks ... I like the old apps compared to the new ones that apparently we are able to upgrade to for free
If only I could find where those snitch rules are stored!!

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Can't launch any app in Mavericks

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