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AEM 6.0 ships with a compatibility option to run the server with the repository technology that is used in AEM 5.6.1. The documentation also refers to it as CRX2 or Apache Jackrabbit 2.x.
AEM 6.0 introduces the next generation Java Content Repository that the documentation refers to as Apache Jackrabbit Oak or CRX3. It comes with many significant improvements, mainly with regards to scalability, performance and optimizations for AEM capabilities. For more info, please see Introduction to Oak.
Adobe is planning to remove the compatibility option in the next release of Adobe Experience Manager. The update process of the next release will contain the option to switch to the Oak-based repository during the update, that can be used for customers that want to update from AEM 5.x or AEM 6.0 using the compatibility option.