I had the same problem (missing applications and files) after upgrading to OS X 10.11.4.
Here was my solution...
1) Reboot into another "user" on the Mac if you have one. In my case, I had earlier created a second "user"... However I think (hope) that the built-in secondary "Guest" account will work for this purpose. Pardon the pedantic instructions to follow if you're an experienced user, but just in case you're a beginner... To reboot into another "user" (or the "Guest" account), go to the Apple menu at the top left and then select the bottom choice to "Log out..."
2) Once you're in the other "user" account on the same Mac, in the Finder, click the "Go" menu and then the "Go to Folder..." selection (second from bottom). Then type in this without the parentheses ( /private/var/folders/ ) and click ok.
3) Once you see the contents of the folder, delete all folders EXCEPT the "zz" folder. Again, do not delete the "zz" folder. Not to be your overprotective mother, but once again, do not forget to IGNORE and DON'T TOUCH the "zz" folder. All others should be dragged to the trash, and empty the trash. You may be asked for an account and password to do so: Use the name of your usual account and its corresponding password. If it says it can't delete certain files, don't worry. Just leave them in the trash for now.
4) Now logout from the secondary or "Guest" account, and log into your usual account. If you are like me, you are suddenly back in business — all your files and folders and applications should suddenly reappear. You may thank a higher power at this point even if you're not a believer. This worked for me, so I hope it will work for you.
Randy