Q:

My Today Extensions in El Capitan are all missing

I was using my Mac over the weekend when I decided to change the song on iTunes from the Today Extension in the sidebar. I swiped to bring the sidebar into view and

Hmm... not there (also no Weather, etc.) OK, I'll open up the Edit interface and

ok, nothing there either. I'll just open up "Extensions" in System Preferences and turn things on

Nothing there either (there should be a fourth entry on the left hand side for "Today Extensions")
I have a second machine at work that doesn't have these problems. Both on the same version of El Capitan.
In the interest of full disclosure I am running El Capitan 10.11.1 beta 3 because I didn't opt out of beta updates to the GM quickly enough (was on beta 1 when I first noticed) but like I said my work machine is on the same version/beta and doesn't have these issues. And I was on beta 1 for days before I noticed. 
Any idea what I can do to get my extensions back?
(also, my Time Machine backup outgrew my hard drive so rolling back isn't an easy option)

A:

Figured it out. 
There's some solutions for Yosemite I found online but none of them worked for me. 
Turns out part of the issue is that El Capitan introduces System Integrity Protection (SIP) which is causing the bug, or it's preventing the fixes from working, or something. 
Anyway I got the answer from here. Basically you just

Reboot in Recovery mode (CMD+R at the chime)
From the recovery menu pick Terminal
Run this command to (temporarily) disable SIP: csrutil disable
Reboot into El Capitan
Verify that the extensions are back in the sidebar and in system preferences
Reboot in Recovery mode again
At the Terminal re-enable SIP with run csrutil enable
Reboot back into El Capitan. Everything should still be back and all is well. 

