FIX: Dangling Nested Catalog Mountpoints in Corrupted Catalogs

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. 
Later it turned out, that the same catalog also contains a *nested catalog mountpoint* that does not have nested catalog registered to it but directly contains the file system contents. This is now fixed as well by removing the *nested catalog mountpoint* flag from this particular entry. In the specific case of **cms.cern.ch** this missing catalog is regenerated directly after the catalog migration due to the *.cvmfsdirtab*.

The migration of **cms.cern.ch** is scheduled for 2nd of September 2014 and we are going to need this fix by then.