In amongst the tens or hundreds of thousands of files which together make OS X El Capitan work, there are security and other settings files which Apple normally updates silently. These are almost completely undocumented, but can sometimes cause problems, by disabling an old version of Flash, Java, or Silverlight, or even breaking your network connection. Here’s a quick roundup of those which you are most likely to come across.
Gatekeeper Configuration Data
Latest version: 156, 30 October 2018.
This is an SQLite database which is placed in /private/var/db/gkopaque.bundle/Contents/Resources/gkopaque.db to provide blacklists and whitelists for Gatekeeper’s security system, which checks the code signatures of apps. El Capitan doesn’t have a Gatekeeper ‘disk version’, unlike Sierra and later.
Incompatible Kernel Extension Configuration Data
Latest version: 11.6.1 (frozen and not updated any more).
This is a list of kernel extensions (KEXTs) which will be excluded at startup, and is stored in /System/Library/Extensions/AppleKextExcludeList.kext.
MRT Configuration Data
Latest version: 1.35, 19 June 2018.
This is the settings for Apple’s Malware Removal Tool /System/Library/CoreServices/MRT.app and goes into that app, so that it can remove any malware which OS X detects.
Latest version: 1.0 2100, 28 September 2018.
These are the whitelists and blacklists used by XProtect, as detailed here. They go into /System/Library/CoreServices/XProtect.bundle/Contents/Resources/XProtect.meta.plist and
Although this has not been updated since the original release of El Capitan, I include it here for completeness. These settings are placed in /System/Library/PrivateFrameworks/SystemMigration.framework and /System/Library/Sandbox/Compatibility.bundle, for use by Migration Manager.
Details last updated 30 October 2018.