Came across this: https://derflounder.wordpress.com/2...taller-removes-package-installation-receipts/ The gist of it is that the El Capitan 10.11.2 full installer (not the update or the combo) deletes the contents of the /var/db/receipts directory, which is a record of the software installed (after the initial install?) on a machine. This would mainly affect those using the installer to upgrade from an OS version below 10.11 to El Capitan. This issue doesn't seem to be widely known (the only web pages I saw referred to the URL above). I can't confirm its veracity but thought it should be brought up here. (I do know the App Store update from 10.11.1 to 10.11.2 does not have this issue.) It was reported to Apple but it's been consolidated into another bug report so the person who reported it in derflounder doesn't know the what's happening at Apple to address this. I guess the workaround would be to save the receipts directory and restore it after the install although who knows what other similar subtle (most users would never know this has happened) issues exist in the installer.