Bottom row of system preferences (third party apps) not showing
I installed homebrew http://brew.sh/ and osquery https://osquery.io/. Then did

select * from preferences where domain like "%system%";


which showed a list of preference settings that might be interesting. ThirdPartyCount was 0, which I thought was wrong. So I backed up ~Library/Preferences/com.apple.systempreferences.plist and used XCode to edit the value to 3 (which is the value I expected). After a reboot it went back to zero.

After more googling, I found /Library/PreferencePanes contains third party preference panes. The aliases in there were all broken: because I'd manually deleted browser plugins from "/Library/Internet Plug-ins". So i deleted the really-dead aliases, re-installed Java and now the bottom row is displaying as expected. Thanks for all your help.

(footnote: AirDisplay used to have a prefpane i think but the latest version not longer has it)