Update 10.11.1 erased all my apps!!!!

have you tried booting into safe mode? That can clear caches out, and run a repair on your hard drive as well. If that does not work you could try re downloading in recovery mode. Sadly at the end of the day, back up, back up and back up again. External drives are cheap, there is really no excuse for not having a back up in this day and age.

same for me, the only solution I have found was a restore from Time Machine. Strangely al the other user profiles were working properly.

Have you solved it by any means?

I had the same problem. Safe mode, Disk Utility repair in Recovery Mode, and Reinstall did not work. I have been traveling and have no access to backups to do a restore.

As I poked around I noticed that over time document folders were missing files and subfolders -- but they appeared eventually if I waited long enough and were later immediately visible when the enclosing folder was opened. That suggested a directory-level problem, which was supported by the applications being visible in another user account.

I solved the problem by copying the Disk Utility app from the user account on my computer and ran it in the original corrupt account. Immediately Disk Utility's window showed the correct file size for apps, photos, music, videos that had been zero. Opening my Applications folder I found all of the apps were now visible, where previously there had just been an empty Utilities folder. Apps opened and ran correctly.

My dock icons were still showing as something like textedit sheets, but opening each app in the dock, including those that had no icon at all, restored the icons.

I am wondering whether the problem is related to how permissions are handled in El Capitan, and the upgrade to 10.11.1 messed up access to the user account files.

I assume you have previously run Disk Utility in Recovery Mode and reinstalled the OS X in Recovery Mode. (To invoke Recovery Mode: Shut Down computer. Start computer via power button, immediately holding down Command R until the Apple icon appears.) These steps didn't solve the problem for me, but you may be fortunate.

If you previously enabled Guest User on your computer, you will be able to copy Disk Utility from there to a USB drive. (From your account, select Apple menu > Log Out..., which will then present Guest User as a login option.) Otherwise, I believe you will need to get Disk Utility from the Mac computer of a friend or colleague. The current version is 15.0. Another option is take your computer to the Genius Bar at an Apple retail store and share this thread with them.

I dragged the copy of Disk Utility from the USB drive to the desktop of the corrupt user account. (I didn't trust putting it in the Applications folder because of the Finder operations that might result.) I then double-buttoned Disk Utility to open it from the desktop and selected the First Aid option.

Either your problem is more extensive or has a different cause from what I encountered. I would suggest at this point going to an Apple store. Apple support suggested this option to me -- make clear that the problem was caused by Mac OS 10.11.1 installation.

If the Apple store can't help, a disk recovery service may be able to extract files before you erase the disk and reinstall from scratch. Do a web search for "<city near you> data recovery" and take the computer to them.

Keep in mind if you have been using iCloud for mail, contacts, bookmarks, photos, etc., these files can be restored easily after your computer is working properly again.

Do we know what the root cause of this is? Do you think there are any preventative measures that can be taken so that new users logging on to the system aren't affected? We have this happening in a enterprise environment for users with mobile accounts (description of our setup/problem below, almost identical). Bill, your fix works, but I'd prefer to have something proactive in place to prevent the problem from happening.

We have a golden triangle setup with OSX Server 10.6.8 and Microsoft Active Directory running on Windows Server 2008 R2. Our users login and have mobile accounts created for them. It appears that when a machine running El Capitan has a new user log in, their desktop loads very slowly. The dock takes about 5-10 minutes to appear and when it does, all the usual icons appear as a white paper with a pencil a ruler. Attempts to open an application on the dock result in a message saying something along the lines of "you can't open application INSERTPROGRAMNAMEHERE because it may be damaged or incomplete". No applications are listed under Applications and Spotlight doesn't work. This only happens for SOME users that logon for the first time to the machine.

Yes, the symptoms you report are identical to what I experienced. I'm glad the Disk Utility fix worked for you. I'm not an OS or Mac specialist so unfortunately I don't have any other information. I'd advise anyone with this problem to contact Apple directly so they are aware it is happening.

I didn't have to repair permissions for some of our users today. Just had to wait a bit. I have to revise my initial description of the problem a little.

"Attempts to open an application on the dock result in a message saying something along the lines of 'you can't open application INSERTPROGRAMNAMEHERE because it may be damaged or incomplete'. No applications are listed under Applications and Spotlight doesn't work. "

The above statement is partially true. After about 15-20 minutes (dependent on spec and age of machine), the Applications folder in Finder changes from being empty, to showing all of the installed Applications with normal icons. I am able to open programs normally, and spotlight becomes responsive again. The icons in the dock still appear as a white paper with a pencil, paintbrush and a ruler, and the only fix appears to be to reset the dock (in terminal running "defaults delete com.apple.dock; killall Dock"), except for the Pages, Numbers, and Keynote icons which show up as question marks.

We are running into this issue not because we're upgrading Macs to 10.11, but because the new Macs we order are coming with 10.11 by default.