Macbook Pro mid-2012: All applications are "damaged or incomplete", question mark on all apps, no icons Over the past couple days I have experience truly the most bizarre issue with an Apple product I have ever experienced. It has a somewhat long story to it, so I have all relevant details in chronological order.

First off, here's my specs: Macbook Pro Mid-2012 i5 w/ 250GB SSD, 1TB HDD in optical bay, 8GB RAM. Running high sierra 10.13.2

Alright. So, my computer installed some updates overnight last weekend. Worked fine the next day, except that Spotlight stopped indexing my applications folder. Rather annoying, but not completely bizzare. I tried fixing it by adding the applications folder to the Spotlight blacklist, then remove it. That did nothing.

Monday night, I tried the following three commands to try to force it to reindex my entire drive: 

sudo mdutil -i on / 
sudo mdutil -i off / 
sudo mdutil -E / 


That did nothing immediately - again, unsurprisingly. But the next day, it still hadn't indexed the drive. The progress bar in Spotlight was stuck at the beginning.

Last night (Tuesday) was when the really bizzare stuff started happening. I tried to launch Fusion 360 (CAD software) from the dock, to be greeted with a "Fusion 360 cannot be opened because it is damaged or incomplete." I did the reasonable thing, and did a system reboot. I tried opening other software from the dock, but was greeted with the same message for all items in the dock. I then tried opening items from the launchpad, only to be greeted with no apps having icons whatsoever. Same thing with apps directly from my Applications folder - attempting to open any app, including system utilities like Terminal and Disk utility - resulted in the same damaged or incomplete error. Additionally, all the apps had their icons missing in the Applications folder. Right-clicking > show package content > browsing to the actual executable also does not work - it asks what software you would like to open the file with. I would have launched them from the terminal, but... well... I can't open it!

At this point, I got seriously freaked out about a corrupted drive, malware, etc, so I shut it down for the night. Today, I pulled the drive and took a full image of it for backup purposes. After some SMART analysis and the massive copy without any errors (used ddrescue on a linux box to clone the drive to an iso), I can say definitively that the SSD is not dying. After backing up the drive, I booted off a recovery USB drive and ran first aid on the main partition on the SSD, which found no errors.

I also tried other user accounts. First I tried another admin account, and google chrome launched on login fine, but no other software would open. After quitting google chrome, it refused to open again - same damaged or incomplete error. I then tried the guest account, where all the app icons on the dock are replaced with question marks. Again, nothing would open. However, I could open "About This Mac", and get a system report, etc. Clicking on software update results in a cryptic error about not being able to find the app to open that link with.

I also know that it isn't a broken SATA cable, as I've booted off a clone of the drive via USB and it has all the same issues.

At this point, I plan on doing a full OS reinstall and copying stuff back from my disk image. But if anyone has any idea why this happened in the first place, or what I could do to repair it short of doing a full reinstall, let me know. If you want screenshots of any of this weirdness (taken with a phone camera, because Preview can't open to take screenshots...) then let me know. Thank for any help!
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.