The check command should do deep traversals by default

Only checking accessibility of the root nodes doesn't make much sense. Even more so because the file store automatically rolls back on startup if a root revision is not accessible. In terms of not doing full traversals, it is more interesting to restrict by path (aka OAK-5556).

The --deep option will still be accepted, but there will be a failure when it is specified. An explanation that full traversal is now done regardless of that option will be printed.