FIX: Corrupt Nested Root entry Handling in Catalog Migration

This problem first showed up in **cms.cern.ch** where two nested catalogs were containing a root directory entry that was flagged as both a *nested catalog root* (which is okay) and a *nested catalog mountpoint* (which does not make sense). For now I have no idea how this situation occurred in the legacy catalogs. However, this change in `cvmfs_swissknife migrate` can detect and fix this issue while migrating the catalog. The migration of **cms.cern.ch** is scheduled for 2nd of September 2014.