The data directory is /var/lib/rkt, unless configured otherwise.
For details, see the paths kind in configuration documentation.
The --dir command line option can be used to change this location.
The CAS database is stored in /var/lib/rkt/cas/db.
The database schema can be migrated to newer versions (#706).
The CAS also uses other directories in /var/lib/rkt/cas/.
To ensure stability for the CAS, we need to make sure we don't remove any of those directories or make any destructive changes to them.
Future version of rkt will retain compatibility with older CAS versions.
The pods are stored in /var/lib/rkt/pods/ as explained in Life-cycle of a pod
The stability of prepared and exited pods is desirable, but not as critical as the CAS.
The configuration on-disk format is documented separately.