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I found MDR caches in $userdir/config/MDRepositories/Storages/org-netbeans-java/ whereas they should be in e.g. $userdir/var/cache/MDRepositories/Storages/org-netbeans-java/.
BTW "storages" is not an English word. Probably you meant just "storage".
Fixed. Now the caches are stored under $userdir/var/cache/mdrstorage/.