OSX 10.11.3 Update - All Applications Gone - Safe boot as well

remove ALL external devices except keyboard and mouse

reset SMC as per this Apple Computer article and proceed with resting the PRAM/NVRAM at the bottom of the same article

Resetting the System Management Controller (SMC) on your Mac - Apple Support

boot into safe mode with all devices still disconnected

Try safe mode if your Mac doesn't finish starting up - Apple Support

if your computer is still "bricked" you have three options.

1) try and find what the cause is and step by step hope you can remedy it.

2) If you have a time machine backup use it to restore your system to a previous state by booting into recovery mode and restoring that backup

Use Time Machine to back up or restore your Mac - Apple Support

and 3) if this is not possible and you have no other option use system restore or internet restore to bring your computer back to a factory state.

your current OS and it's data will be destroyed unless you can perform this on another HD or another partition which is clean/empty.

OS X: About OS X Recovery - Apple Support

Before you take drastic measures, you may want to try this:

1) Uninstall the antivirus completely (and make a note never to reinstall that)

2) Download the combo update and run it.

Antivirus on the mac only serve to hinder performance and cause trouble; and the same should be said about most programs that claim to "clean" your drive. Run, don't walk, away from those.

I see that you are a person who takes security very seriously.

I can't object to that, of course.

But I do see computing in a different perspective.

The number of mac virus in the wild is zero. Antivirus are known to cause problems and degrade performance, so I choose never to use that.

If you deal with sensitive data that must be kept secret, then File Vault is probably a good idea. I have, however, seen a few horror stories of users who have lost access to their data. My fear of losing my data because of File Vault issues is greater than my fear that someone else may access my data for lack of encription.

Louis is correct in this.

Mac AV is not Window AV as Mac OS in not Windows. A windows centric approach to security is a recipe for disaster on the mac and while Windows developers work with many of the commercial AV development process mac OS does not. I've tested a dozen mac commercial AV products for companies and before I even started using these forums my findings were they are disastrous.

and while you have posted a significant number of good reads none of these potential points of failure have either made it to distributed code, or a white paper as a theory and none of these commercial AV products have any track record of thwarting these potentials in a real life situation if they did suddenly find distribution outside of a securities lab. What they do have however is a undeniable history as to the root cause of OS X instability as reported by countless users on these forums who have discovered removing the offending AV has cleared up a litany of issues but not offered any real security.

docgoku wrote:

I believe the important issue is the Claim AV based on comments I found in a few news articles.

Apparently some AV suites have fought this update on install.

I can assure you that ClamXav was not responsible. I provide uncompensated Tech Support on the ClamXav Forum and have access to all the Help Desk Tickets that have been filed to date and there has not been a single report concerning such a problem, other than yours. I have also personally installed 10.11.3 multiple times on my computer without issue.

I would have to agree that some A-V software has been shown to interfere with new security features in El Capitan and developers are scrambling to fix the problem, but since ClamXav has no Kernel Extensions and only one background process (Sentry) which quits before installation begins, there is nothing to interfere.

docgoku wrote:

My opinion, OSX is just as/if not more prone to attack as windows/linux/ect.

I can't disagree that OS X is probably as prone to attack as those other platforms, but numbers to date show that it's not yet under attack to the extent that Windows platforms are. According to one Security specialist that post here frequently, there were only four new OS X threats (other than Adware) discovered in 2015. That's the lowest it's been in several years now.

Not sure why you posted the hackread article about targeted attacks against social rights activists in China and well as Indian / Russian government agencies that were all Windows based. There have been targeted attacks against minority sympathizers who are OS X users, but all the ones we know about were using very old vulnerabilities that were patched years ago. I suspect the hope was these targets were using obsolete systems.

As you say, none of this contributes to solving your current issue, but I would be happy to discuss the facts with you once you are back in business.

if you are running Mac Office 2008 and you have not patched since 2009 your system is vulnerable to the attack you mention by name, especially if you are a Tibetan activist, otherwise if your an activist running running a patched MS office 2008 or more likely your an activist running something like Open Office or Libre Office (because what true activist is going to give money to MS when you can download a freeware suite that does the same thing and stick it to the man in Redmond) this malware exploit is totally and completely useless more than it is remote.

I had this exact same issue. My regular user account had bad application icons. Applications could not be launched using any of the normal methods. Logging into my admin' account (regular one is just a user for better security...) everything worked fine. I tried the SMC reset, PRAM reset and ClamAV removal. No joy.

While logged in as my regular user account, inadvertently, I double clicked on an HTML file and FireFox (my default browser) launched normally. It was slow to launch, but it launched normally. That continued to confirm that the fundamentals were all still there in the system and for this user. I started looking for linkage, directory, listing or similar types of problems and solutions.

Eventually, I stumbled across threads that talked about the /private/var/folders directory. The following links give you an idea, but you should do your own research:

http://apple.stackexchange.com/questions/209266/el-capitan-private-var-folders-c ache-files-consuming-30-40-gb

http://www.magnusviri.com/OS_X_Admin/what-is-var-folders.html

https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/ man7/hier.7.html

I had changed my regular user temporarily to an admin' account. I closed all open applications. I navigated to the /Private/Var/Folders directory. I deleted everything EXCEPT the zz/ directory. (Yes, my DOS roots are showing, but using the word folders to talk about a folder named folders is awkward.) The final step was doing a Shutdown (not logout, sleep or otherwise.) When I logged back in, EVERYTHING was back! Subjectively, the machine seemed more snappy (faster.) It was certainly faster than the broken and lost Applications state. For my own security conscience, I reinstalled ClamAV,logged out, logged in to the proper admin account, set the regular user back to just a user, did another shutdown and finally logged back in to the normal user account.

It's all back the way it should be. No rebuild required. The circumstances of the failure were likely caused by a conflict of the 10.11.3 patch and ClamAV. The fix is straightforward, once you know what to do. I hope this helps others.