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...