Upgrading to OS X El Capitan using the OS X 10.11.2 installer removes package installation receipts
Following the recent release of OS X El Capitan 10.11.2, it appears that the OS X 10.11.2 installer has an unexpected and unwelcome behavior. When upgrading from an older version of OS X to OS X 10.11.2 while using the OS X 10.11.2 installer, the /var/db/receipts directory is being removed as part of the OS upgrade process. This directory is used by OS X to store a database of receipts for software installed using an installer package, which provides a historical record of what software has been installed on a particular Mac.
The removal of the receipts database is particularly problematic for software installation management tools like Munki and Simian, as they leverage the information in the receipts database to determine which software has been installed (or not installed) on a particular Mac. Other system management tools that leverage the receipts database may be affected by this issue as well.
As this behavior appears to be coming from Apple’s OS X installer, this behavior has been observed in both Apple’s OS X installer and in OS X installer packages generated by createOSXInstallPkg.
A bug report has been filed with Apple about this behavior by Mike Solin. For those who want to file a duplicate report, it is bug ID 23853195. The information in the bug report has also been posted to Open Radar, available via the link below:
http://www.openradar.me/23853195
Fortunately, this behavior does not appear to apply to Apple’s OS X 10.11.2 updates for Macs already running OS X El Capitan. Updating from OS X 10.11.0 or 10.11.1 to OS X 10.11.2 using Apple’s OS X El Capitan 10.11.2 Update or OS X El Capitan 10.11.2 Combo Update does not result in the /var/db/receipts directory being removed, meaning the existing receipts database remains in place and is not deleted.
For those who want to provide upgrades from older versions of OS X to El Capitan and want to avoid this problem, the best course of action at this time is to do the following:
- Use an OS X El Capitan 10.11.0 or 10.11.1 installer to upgrade the Mac in question to El Capitan
- Following the OS upgrade, use Apple’s software update tool to update the Mac to OS X 10.11.2
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Der Flounder 
Fortunately this does not seem to be affecting the receipts for things installed by Casper!
I wasn’t able to reproduce this upgrading from 10.9.5, FWIW.
First I thounght: no problem, just restore it from TM. But the system files are no longer accessable ! Maybe if you disable SIP ?
You can find the receipts in /System/Library/Receipts/