Macbook Pro mid-2012: All applications are "damaged or incomplete", question mark on all apps, no icons
Following your initial description, I had the exact same problem. But it wasn't a malicious cable. So, for future reference and people with this problem, this is my solution, which is way more easier: 

Let's assume you don't even have access to the terminal / console and therefore you have to boot into recovery mode:


(re-)boot into recovery mode (hold CMD + R until Apple logo appears)
start console / terminal
locate the folder /private/var/folders/ of your regular installation (!)


Heads up: 
If you are able to run the console within your regular installation, the folder is just there: /private/var/folders/. 
But if you use the recovery mode console, the /private/var/folders/ is the one of your recovery interface. You need to look for a folder like /Volumes/Macintosh/private/var/folders/ - that's the location of all your regular files. 

If you get to the correct folder, you just delete it's content. (For security reasons you may move the content of this folder to a temporary location). 

After your done, just reboot. This should fix your problem. 

Nota bene:

As far as i know /private/var/folders/ just contains a lot of temporary files which will be deleted every time you restart your mac. If you are using the hibernation mode, this folder may grow constantly. It also could help to reboot the system while holding the SHIFT-key, as this also runs a few routines that will clear temporary files.