Hello,
those folders didn't get removed, but they are no longer contained in the web application in an exploded format (on the file system). They are now contained in the JAR(s) of the Alfresco sub-project / addon they originate from. The core Repository subsystems should be contained in the alfresco-repository-xx.jar
The way to configure subsystems remains the same - create a subsystems folder structure in /shared/classes/alfresco/extension and drop in your custom Spring context or properties files as you did with previous Alfresco versions.
Regards
Axel