OAK-1760: RepositoryUpgrade leads to one large commit with DocumentNodeStore causing OOM

Fix problems introduced in the earlier fix:
Do the JCR_SYSTEM exclusion check only at the root level.
Override defaults instead of merging them with content from the source repository.

git-svn-id: https://svn.apache.org/repos/asf/jackrabbit/oak/trunk@1589748 13f79535-47bb-0310-9956-ffa450edef68